Dear 闽乐 ,

We have fixed some possible issues in Adenita - it should be updated automatically for you. Could you please check whether it works for you?

Hello,

Although I have re-install Ubuntu with 200GB mounted in /, it still stoped around 29

When I run %df -l, it showed below

Filesystem 1K-blocks Used Available Use% Mounted on
udev 131770300 0 131770300 0% /dev
tmpfs 26361104 2888 26358216 1% /run
/dev/nvme0n1p2 191197068 11936596 169478456 7% /
tmpfs 131805512 46716 131758796 1% /dev/shm
tmpfs 5120 4 5116 1% /run/lock
tmpfs 131805512 0 131805512 0% /sys/fs/cgroup
/dev/loop0 9216 9216 0 100% /snap/canonical-livepatch/132
/dev/loop2 289280 289280 0 100% /snap/pymol-oss/98
/dev/loop1 113280 113280 0 100% /snap/core/12834
/dev/loop3 33152 33152 0 100% /snap/snapd/12704
/dev/loop4 63488 63488 0 100% /snap/core20/1405
/dev/loop5 66688 66688 0 100% /snap/gtk-common-themes/1515
/dev/loop6 254848 254848 0 100% /snap/gnome-3-38-2004/99
/dev/loop7 56832 56832 0 100% /snap/core18/2128
/dev/loop8 224256 224256 0 100% /snap/gnome-3-34-1804/72
/dev/nvme0n1p3 758522328 506548 719415232 1% /home
/dev/nvme0n1p1 9755312 5384 9749928 1% /boot/efi
/dev/nvme1n1p1 960379920 77856 911447640 1% /home2
/dev/loop9 52224 52224 0 100% /snap/snap-store/547
tmpfs 26361100 20 26361080 1% /run/user/125
tmpfs 26361100 44 26361056 1% /run/user/1000

I think it is not a space problem though, I don't know how to solve this problems.

please help,

Great, thanks! I will also mess with transparency, etc. in order to see some interactions in more detail.

Thank you for your quick response, it is much appreciated!

Hi Nick, thanks for the posts, we've sent you messages about how to reach us for chat so we can help you.

Yes, it would be useful to have the energy profile along the path. Not only the height of the barrier, but also its width, shape, etc.

Alternatively, you can do this without the Brenner interaction model but with the built-in minimization which uses the Universal Force Field (UFF) and the Add editor (shortcut: A) (it's Carbon by default).

First, you will need to modify SAMSON preferences (Ctrl+K):
-1- For the Add editor, disable the "Adjust hydrogens ..." option.
0_1600418725406_Preferences-Add-no-adjust-H.png

-2- For the Minimization, disable the "Warn me when hydrogens appear to be missing" warning to prevent it from poping-up on each new bond connection.
0_1600418739623_Preferences-Minimize-no-H-warning.png

Then you can apply the minimization: Home >Simulate > Minimize. Start connecting atoms in the nanotube and the graphene sheet using the Add editor (A) - to create a bond simply connect two atoms with this editor.

Indeed in the current version of the Gromacs Wizard, you will need to have a force field which allows for both biomolecules and CNTs. Then you can add such a force field in the settings of the module. However using a 'one-shot parameterization' (e.g. using the ATB server) will not work at the moment with the Gromacs Wizard.

Thanks Dear.

Dear @DmitriyMarin
Thank you for your reply!
Yes, that LAMMPS wizard would be wonderful.

Best regards,
Patrik Molnár

Hello,

The issue is that SAMSON was installed as Administor. Can you please try to activate User Access Control (UAC) so that Windows does not install SAMSON as admin? Here's a link about how to do that: https://www.technipages.com/windows-enable-disable-user-account-control-uac

Please set UAC to e.g. "Always notify" (you can set it back to the previous setting afterwards).

0_1586188022427_b58888db-0b85-4f3f-8459-6d51649a09ab-image.png

Then, please restart your computer, and install SAMSON again.

Please let me know how this goes.

Thanks,

Stephane

Thank you so much for helping me. I tried to link exactly Qt5.12.5 (my own version is 5.14.1) so it works now. Again, thank you so much.

Best regards,

Dong.

Dear John,

As Stephane pointed out, Adenita is for now compatible just with SAMSON 0.8.5 or 0.7.0, for Windows and Linux. But there are plans to port it to SAMSON 2020 and Mac, I expect this versions to be available during April this year.

Best regards,

Elisa

Dear @Yair-Augusto, Adenita was just updated and this problem should have been fixed. Please let me know if it persists or you find new ones.

Best regards,

Elisa

It does! Thanks a lot.

Dear @sudhir ,

For the protein-ligand simulation, you can check out the Ligand Path Finder tutorial for Ligand Path Finder Element. You can also check out the Ligand unbinding pathway search tutorial for the free Ligand Unbinding Search Element (available only on SAMSON 0.7.0).

As for saving MD trajectories, you can check out the tutorial on exporting atoms trajectories along paths which uses the Export Along Paths Element. This Element allows you to export trajectories into PDB files which you can further analyze using other software.

You can also do some analysis and post-processing in SAMSON thanks to the Python Scripting Element, you can check out the Python Scripting guide for more information, for example, the Computing RMSD sample.

To simulate a protein-membrane complex you can use the GROMACS Wizard Element, using this Element you can easily prepare your system for GROMACS simulation, minimize and equilibrate the structure, and simulate your system using GROMACS. See the GROMACS Wizard tutorial for more information.

Hi,
Actually interactive fitting only VMD is providing and that is also very limited. VMD chops off your actual EM map according to the provided pdb model instead of fitting it into the density.
So, as I want to fit multiple structures in the map, I can not do it. I was trying to fit my multi-chain PDB in the same map but it failed.

Chimera do not provide interactive fitting and it fits the protein poorly in the map. Therefore, it is hard to get a proper knowledge of the conformation of any of these tools.

Rest tools are more programming centric, making them hard to be used by biologists having limited programming skills like me.

Dear Stephane,
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.

Sorry, SAMSON needs a 64-bit computer to run.

Dear Stephane,

Yes, we have atoms. The 0.8.0 solution will be the best long-term, as we are dealing with large systems and FPS drop a lot when translating or rotating, but for now I will check the ParticlePositionChanged event.

Thanks!!

Elisa