Re: [gmx-users] Cannot find gmx_mpi when installing gromacs 5.0

I'd guess your permissions on some part of /users/yli/gromacs-5.0/exec/bin/gmx_mpi are such that you can't access. Mark On Thu, Aug 28, 2014 at 4:06 AM, 朱文鹏 jasonzhu...@gmail.com wrote: Dear all, I am trying to install gromacs 5.0 by cmake on my cluster. But an error occurs when I make

Re: [gmx-users] md simulation steps

No :-) It depends what you are trying to observe; generally that's statistical in nature and you thus need to make a large number of independent post-equilibration observations from a converged trajectory. Doing that is generally quite difficult - you should be guided by what previous people have

[gmx-users] water not getting settle

Hi everyone , I am getting an error about water i.e step 168: Water molecule starting at atom 5226 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have already tried reducing timestep ..but it didn't worked . If I freeze water things work fine . But what

Re: [gmx-users] water not getting settle

Depends what the problem really is. See strategies at http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Thu, Aug 28, 2014 at 9:35 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone , I am getting an error about water i.e step 168: Water molecule starting at

Re: [gmx-users] Time varying electric field - phase term

Or, can you wait a while before you turn on the field? So far, I know that people can do npt after nvt. Can you run simulation without field, then, with field? Just have to count the delays. There might be some truncation effect tough if you turn on the field suddenly. On Wed, Aug 27, 2014

[gmx-users] MD exit condition

Hello Gromacs users, I am using Gromacs 4.6.5 Is there a way to set an exit condition during a simulation? I am interested in terminating dynamics when two groups are separated by a certain distance. If it is not possible to set an exit condition, I suspect I can post process the trajectory

Re: [gmx-users] Cannot find gmx_mpi when installing gromacs 5.0

Dear Mark, Thank you for your response. But I can install gromacs 4.6.5 successfully with the same permission. I will still contact the administrator of the cluster. Do you have idea what permissions I should ask them for if I need to install 5.0? Any files or directories, or any permissions to

[gmx-users] GB parameters for DNA

Dear everyone, I would like to simulate a DNA-protein complex using implicit solvent model. Anyone has the GB parameters for phosphorus atom?  I searched the mailing list, but did not find the answer. Thanks in advance Cheers, Jianguo -- Gromacs Users mailing list * Please search the

[gmx-users] Positive Potential Energy.

Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum

[gmx-users] Surface tension for membrane simulation

Hi all, I have a question of surface tension in membrane simulation. I found that in equilibration and production step, the pressure set up for membrane simulation is below: ; Pressure coupling is on pcoupl          = Parrinello-Rahman         ; Pressure coupling on in NPT pcoupltype      =

Re: [gmx-users] Positive Potential Energy.

On 8/28/14, 2:04 PM, Dan Sponseller wrote: Hello everyone. I am still fairly new to gromcs but I have researched this well. I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even

Re: [gmx-users] Positive Potential Energy.

Hey Daniel :) This doesn’t make sense as the molecule should fly apart with always positive PE. You need a force to make things fly apart, but the force has little to do with the absolute PE. It's the gradients that do it. And as Justin points out, your system can choose between positive PE

[gmx-users] GPU Acceleration in case of Implicit Solvent Simulations

Dear all, Can we use periodic boundary conditions in case of implicit solvent simulations? If so, why? Also, can implicit solvent model in gromacs in any version (till 5.0) be implemented in more than 2 processors or can it at least use GPU acceleration provided by gromacs? I have tried using

[gmx-users] Martini force field for inhibitors

Dear Gromacs users, I have very recently started working with Gromacs and Martini force field. I am able to generate the coarse-grained model for HIV Protease (1hvr.pdb). I want to simulate the protein along with its inhibitor. Are there any guidelines for building (coarse-graining) its

[gmx-users] g_select syntax

Hi Everyone, I am recently puzzled by the syntax and behaviour of g_select. I want to obtain the residue index list of LIPID whose center of mass is within 1.0 nm of the surface of protein. In my case, each LIPID molecule consists of only one residue. I wrote the selection.dat as follows, and set

[gmx-users] Water droplet moving away from surface

Dear all,I am running an equilibration calculation using a new force field (GRAPPA), for a 10,000 water molecules on graphene. The run is up to 378 ps now. Iam concerned that the water droplet will drift away from the surface, rather than forming a nice droplet.Is the cutoff values in my