Re: [gmx-users] how to visualize gromacs trajectory

Hi, Yes that command is right. If you need to do other commands, the trjconv description and options are in the second link I gave: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html Regards, Stephani On Tue, 9 Jul 2019 at 00:13, sunyeping wrote: > Hello, steph, > > I

Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb

On 7/8/19 7:31 PM, Carlos Navarro wrote: Dear gmx-users, I was wondering if someone can share the Berger parameters for POPC for Amber99sb (and I they can share also a .pdb .gro file will be even better). I found several for gromos, but I need them form AMBER99sb. Berger parameters are

Re: [gmx-users] Repeat Simulation n times

On 7/8/19 1:43 PM, Neena Susan Eappen wrote: Hello gromacs users, To repeat a simulation say 50 times, do I manually start from minimization step to data collection 50 times, or is there anything I can write in the command line? To run 50 independent simulations, I would run minimization

Re: [gmx-users] rigid body motion

On 7/8/19 11:54 AM, Morteza Chehel Amirani wrote: Hello, I'm just wondering what is the best way to put constraints on a group of molecules (several water molecules + ions) to move as a rigid body i.e., to keep the relative distance between atoms of the group fixed? The water molecules and

Re: [gmx-users] NVT ensemble for simulating of carbon nanotube (as drug delivery)

On 7/8/19 3:22 AM, afsaneh maleki wrote: Hi all I have two questions: 1- Is it correct to apply statistical ensemble NVT (N=constant, T=constant) for simulating of carbon nanotube (as drug delivery)? It doesn’t leads to a pressure in the system that is far from normal pressure? Some

Re: [gmx-users] gromacs pullcode

On 7/6/19 9:17 PM, zhaox wrote: Hi, There are two  groups in my system.When I use the pull code to pull one group along the axis X, setting pull_coord1_geometry =direction,I am confused with the "distance at start" and the "reference at t=0".Could anyone can tell me how to understand

[gmx-users] POPC Berger lipids parameters for AMBER99sb

Dear gmx-users, I was wondering if someone can share the Berger parameters for POPC for Amber99sb (and I they can share also a .pdb .gro file will be even better). I found several for gromos, but I need them form AMBER99sb. Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic

Re: [gmx-users] About 2019 GMX manual

Dear Benson and Paul, Thank you both very much. I will open the issue in redmine and, Benson, I'd appreciate if you could act on my behalf at gerrit. Best regards, Alan On Mon, 8 Jul 2019 at 03:37, Paul bauer wrote: > Hello, > > as Benson said, please open an issue at redmine.gromacs.org for

[gmx-users] Repeat Simulation n times

Hello gromacs users, To repeat a simulation say 50 times, do I manually start from minimization step to data collection 50 times, or is there anything I can write in the command line? Thank you, Neena -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Self-interaction across periodic boundaries

Thanks Mark. The problem is that I would like to keep the overall concentration constant, so, using a larger box e.g. with 2 times larger lateral box dimensions, needs me to increase the number of molecules 8 times, so even more likely to lead to percolating structures in a larger simulation box.

[gmx-users] rigid body motion

Hello, I'm just wondering what is the best way to put constraints on a group of molecules (several water molecules + ions) to move as a rigid body i.e., to keep the relative distance between atoms of the group fixed? The water molecules and ions form a droplet in my simulation and I would like to

Re: [gmx-users] how to visualize gromacs trajectory

Hello, steph, I have read the workflow for trajectory fixing at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions, but I don't know how to perform these steps. The workflow reads: First make your molecules whole if you want them whole. Cluster your

Re: [gmx-users] Self-interaction across periodic boundaries

Hi, If you're trying to model something like it was at infinite dilution using a periodic box, then the size of the box needs to be at least as large as the size of the structure and its effective interaction radius. It seems like your simulation is suggesting at least one of those is larger than

[gmx-users] Self-interaction across periodic boundaries

Dear all, Using MD simulations I expect to observe aggregation among some molecules solvated in water to have ultimately a droplet out of the molecules. The aggregates form to some extent in the course of simulation time, however, after a while the system become kinetically trapped in artificial

Re: [gmx-users] Install on Windows 10 with AMD GPU

Thankyou Szilárd, Headers are available here https://github.com/KhronosGroup/OpenCL-Headers But I get CMake Error at cmake/gmxManageOpenCL.cmake:45 (message): OpenCL is not supported. OpenCL version 1.2 or newer is required. Call Stack (most recent call first): CMakeLists.txt:236 (include) I

Re: [gmx-users] About 2019 GMX manual

Hello, as Benson said, please open an issue at redmine.gromacs.org for all kinds of bugs that you find :) (even documentation issues like this)! After this, you can upload a fix for the issue yourself at gerrit.gromacs.org after creating an account there, or one of us will get around to do