Re: [gmx-users] Neutralizing

Thank you Justin for your help. On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul wrote: On 3/9/16 1:42 AM, mohammad r wrote: > Thank you Parham and Justin, Excuse me I have another question, in simulation > of a water-peptide system, is it necessary to use QM/MM

[gmx-users] Fwd: Trouble with mpirun gmx- 2/2 machines not sharing correctly

I've recently installed OpenMPI 1.10.2 alongside GROMACS 5.1.2. I've read all over the web about how to, but I'm having issues left and right. I've finally gotten to a point where *gmx* works, but in an odd way. I'll try to explain without too much detail. Machine1= CPU: 8-core AMD FX9590 GPU:

[gmx-users] How can I control PME domain decomposition

Hi everyone, I am working on PP/PME optimization. But I found while PP ranks could be controlled by, say -dd 9 8 8, PME node decomposition CANNOT be tuned. For instance, below is the basic information for optimization: - Using a fourier

[gmx-users] Beginner Question -- Grab Info from Output

Hi, I am running gmx msd and would like to import the value of the calculated diffusion coefficient and error that is output in my linux terminal. I know I can view the trajectory with grace or parse the file in a text editor for its values, but I would just like end calculation. Is there a way I

Re: [gmx-users] .mtx file

Hi, I don't think the hessian calculation is parallelized. Try running in one core. HTH, Rui Rodrigues De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Em Nome De Alexander Alexander

Re: [gmx-users] .mtx file

On 3/9/16 6:00 PM, Alexander Alexander wrote: Dear Gromacs user, I was wondering why no .mtx file as hessian file was produced in my gmx mdrun? I used below command to submit my mdrun job: gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4 neither md.mtx nor hessian.mtx!?

[gmx-users] .mtx file

Dear Gromacs user, I was wondering why no .mtx file as hessian file was produced in my gmx mdrun? I used below command to submit my mdrun job: gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4 neither md.mtx nor hessian.mtx!? Cheers, Alex -- Gromacs Users mailing list *

[gmx-users] axial velocity autocorrelation

Hello, I am working with a confined system with damped motion of molecules in the x and y directions. Is there a workaround that would allow to calculate just the axial velocity (vz) autocorrelation rather than the total velocity autocorrelation? Best regards, Michelle -- Gromacs Users

[gmx-users] adding windows to thermodynamic integration

Hi everyone, I'm doing a TI calculation for a molecule that's of interest to me and the results after gmx bar processed the dhdl.xvg files aren't so good at certain points so I want to add some lambda values around the problematic ones and I was wondering if this means I have to do the entire

[gmx-users] Steered Molecular Dynamics for citrate channel

Dear gromacs users I want to force the citrate to cross the channel using SMD, but when I run the tutorial Umbrella Sampling for my system adapting the entries mdp for gromacs-5.0.5 my results are staying bad!! I want see citrato crossing the channel, and in the "generating configurations" the

Re: [gmx-users] semi-permeable wall in gromacs

On 3/9/16 12:28 PM, gozde ergin wrote: Dear all, I would like to compute the osmotic pressure directly from all-atom MD simulations of concentrated aqueous solutions. The basic idea is to introduce “virtual” walls to represent the effect of ideal semipermeable membranes, separating a high

[gmx-users] semi-permeable wall in gromacs

Dear all, I would like to compute the osmotic pressure directly from all-atom MD simulations of concentrated aqueous solutions. The basic idea is to introduce “virtual” walls to represent the effect of ideal semipermeable membranes, separating a high concentration region from a pure water

Re: [gmx-users] How the angle/bond length changes during simulation.

On 3/9/16 10:01 AM, Dawid das wrote: Dear Gromacs Experts, How can I get a plot of a bond length/ valence angle/ dihedral angle during simulation from *xtc and *.ndx files? I am pretty sure that it is possible, but with g_angle and g_bond I can get only the distribution. Get the bond

Re: [gmx-users] Neutralizing

On 3/9/16 1:42 AM, mohammad r wrote: Thank you Parham and Justin, Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by

Re: [gmx-users] How the angle/bond length changes during simulation.

O'right, I found my mistake. Now it works fine. Thank you! 2016-03-09 16:11 GMT+01:00 Justin Lemkul : > > > On 3/9/16 10:11 AM, Dawid das wrote: > >> 2016-03-09 16:07 GMT+01:00 Justin Lemkul : >> >> >>> You are. That's what -all is for: >>> >>> "Plot all

Re: [gmx-users] How the angle/bond length changes during simulation.

On 3/9/16 10:11 AM, Dawid das wrote: 2016-03-09 16:07 GMT+01:00 Justin Lemkul : You are. That's what -all is for: "Plot all angles separately in the averages file, in the order of appearance in the index file." Open up angaver.xvg and you will see the average, then the

Re: [gmx-users] How the angle/bond length changes during simulation.

2016-03-09 16:07 GMT+01:00 Justin Lemkul : > > You are. That's what -all is for: > > "Plot all angles separately in the averages file, in the order of > appearance in the index file." > > Open up angaver.xvg and you will see the average, then the two individual > time series.

[gmx-users] How the angle/bond length changes during simulation.

Dear Gromacs Experts, How can I get a plot of a bond length/ valence angle/ dihedral angle during simulation from *xtc and *.ndx files? I am pretty sure that it is possible, but with g_angle and g_bond I can get only the distribution. By the way, when I use g_angle -f npt-md2-cent.xtc -n

Re: [gmx-users] Regarding using random seed

Right! T. On Mar 9, 2016 12:24 PM, "neha chaudhary" wrote: > Hi, > > So all I have to do is to extract different configurations from my already > performed MD simulation. Then I have to prepare a new system using that > configuration with the following parameters and

Re: [gmx-users] Regarding using random seed

Hi, So all I have to do is to extract different configurations from my already performed MD simulation. Then I have to prepare a new system using that configuration with the following parameters and rerun the simulations: continuation = no gen_vel = yes gen-seed = -1 Right? Best Regards,

[gmx-users] Query about a simple MD with constant electric field

Dear Gromacs users I am doing a very simple MD with a constant electric field of 1 V/nm along the positive z-direction in a system containing only one Na+ ion, starting from rest. The ion is not coupled to the thermostat and it is placed in a box of 4 nm* 4nm * 16 nm, in the X,Y,and Z

Re: [gmx-users] Regarding using random seed

Hi Neha, Set continuation = no gen_vel = yes (check http://manual.gromacs.org/online/mdp_opt.html#vel) Best, Tsjerk On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary wrote: > Thanks Tsjerk for replying, > > I want to ask one more question that to start with new

Re: [gmx-users] Regarding using random seed

Thanks Tsjerk for replying, I want to ask one more question that to start with new velocities, what changes I have to make and in which .mdp file? Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal

Re: [gmx-users] Regarding using random seed

Hi Neha, You can perform a simulation first, and then extract configurations, which you simulate with new starting velocities. Alternatively, you can generate a number of different starting structures using elastic-network modeling, like with the ElNemo server. Mind to first energy minimize the

[gmx-users] Regarding using random seed

Hello there, Can anyone tell me how can I start my MD simulations with different starting structure (random seed) for my protein-ligand complex. Can I start with different sets of coordinates and velocities? If yes, how? Thanks, *Neha* Research Scholar, Centre for Computational Biology and