[gmx-users] About the data loss due to Disk space problem

Dear Gromacs Users, I am facing the problem with the output generated during the condition of critical disk space (Both Hard disk and OS associated Memory space). The problem definition is as follows: 1. The .trr and .xtc file generated shows Incomplete frame error in the very beginning of the

[gmx-users] Problem with OPLS parameters (too few parameters on line)

Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I followed the chris neale directives to make the necessary changes i.e. sigma and epsilon, I incorporated the modified atom types of lipids in

[gmx-users] run.mdp on 4.6-gpu

Dear Gmx Users, Could you please assess my mdp file on GPUs: title = Protein-ligand complex MD simualation ; Run parameters integrator = md; leap-frog integrator nsteps = 1; 200 ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr

Re: [gmx-users] Problem with OPLS parameters (too few parameters on line)

On 4/17/13 4:28 AM, Parul tew wrote: Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I followed the chris neale directives to make the necessary changes i.e. sigma and epsilon, I

[gmx-users] position restrained energy minimization

Dear gmxers, As is well-known, molecular dynamics can be implemented with position restrained in gromacs. Now I want to ensure whether energy minimization can also be performed with position restrained. Thanks for any reply to this letter. Chaofu Wu -- gmx-users mailing list

Re: [gmx-users] position restrained energy minimization

On 4/17/13 7:39 AM, Wu Chaofu wrote: Dear gmxers, As is well-known, molecular dynamics can be implemented with position restrained in gromacs. Now I want to ensure whether energy minimization can also be performed with position restrained. Thanks for any reply to this letter. Sure, try it

[gmx-users] Simulations box type

Hello All, I am here not with a problem but still i need your suggestions. I have a linear DNA molecule of 200nm in length and want to rum MD to calculate some bending properties. I want to know ...what kind of solvation box type will be good for such molecule?? Thank you cheers Raghav --

Re: [gmx-users] Simulations box type

On 4/17/13 7:57 AM, raghav singh wrote: Hello All, I am here not with a problem but still i need your suggestions. I have a linear DNA molecule of 200nm in length and want to rum MD to calculate some bending properties. I want to know ...what kind of solvation box type will be good for such

[gmx-users] Autocorrelation of C-N

Dear Users, Could you advise me please how to calculate vector C-N autocorrelation function in my protein along the simulation time? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] trjcat set timestep/amb2gmx?

What do you mean by style 8? On Tue, Apr 16, 2013 at 4:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote: See style 8 for trjconv -h Mark On Tue, Apr 16, 2013 at 10:26 AM, francesco oteri francesco.ot...@gmail.com wrote: Hi, yes Marc you are right but the last time I used gromacs

Re: [gmx-users] trjcat set timestep/amb2gmx?

On 4/17/13 11:06 AM, Steven Neumann wrote: What do you mean by style 8? Did you read trjconv -h? There's an enumerated list in the very beginning. Mark is pointing you towards #8 in that list. -Justin On Tue, Apr 16, 2013 at 4:51 PM, Mark Abraham mark.j.abra...@gmail.comwrote: See

Re: [gmx-users] trjcat set timestep/amb2gmx?

I read it... did not know styles are equal to points :) On Wed, Apr 17, 2013 at 4:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/17/13 11:06 AM, Steven Neumann wrote: What do you mean by style 8? Did you read trjconv -h? There's an enumerated list in the very beginning. Mark is

[gmx-users] how to direct log file correctly?

Hello: I found that each time I submit gromacs job in GPU workstation, the log file always in my terminal screen, like: imb F 1% step 13700, will finish Wed Apr 17 17:57:20 2013 imb F 1% step 13800, will finish Wed Apr 17 17:57:20 2013 imb F 0% step 13900, will finish Wed Apr 17 17:57:20

Re: [gmx-users] how to direct log file correctly?

On 4/17/13 11:30 AM, Albert wrote: Hello: I found that each time I submit gromacs job in GPU workstation, the log file always in my terminal screen, like: imb F 1% step 13700, will finish Wed Apr 17 17:57:20 2013 imb F 1% step 13800, will finish Wed Apr 17 17:57:20 2013 imb F 0% step

[gmx-users] 2d-pmf with plumed gromacs

Dear gromacs user, We want to compute a 2d-PMF for a peptide translocating into a coarse grained water lipid system. We find gromacs patched with plumed could allow us to run 2d umbrella sampling, so we install gromacs 4.6.1 with mpi support, and patch it with plumed 1.3. From plumed

Re: [gmx-users] Re: Viscosity calculation using cos_acceleration

Dear Vitaly and other Gromacs users, Thanks for your reply. That's a good suggestion, and actually one of the first things I tried, though without success. Up to around cos_acceleration = 0.025 the viscosity is constant around 40 mPa.s, and then for increasing cos_acceleration the viscosity