Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

The comment from Justin and your answer to it were pretty convincing. I think the problem is solved :)). Tom is correct to get T with g_energy on a simulation that ran with one Tcoup, you need to rerun the trajectory (trr) with a tpr in which you define two Tcoup. This should give you T for each

[gmx-users] Re: Number of solvent molecules

> Dear users, > > How is it possible to fix the number of solvent molecules and the size of the > box used so that I can maintain exactly the same environment for different > runs. > For eg, if I have 84000 water solvent molecules and the dimensions of 6.7 > 6.73 4.71 nm; how can I use the same

Re: [gmx-users] Number of solvent molecules

P.R.Anand Narayanan wrote: Dear users, How is it possible to fix the number of solvent molecules and the size of the box used so that I can maintain exactly the same environment for different runs. What are you planning to vary? For eg, if I have 84000 water solvent molecules and the dimens

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Daniel Adriano Silva M wrote: Dear Gromacs users, I am experimenting the next problem on an infiniband-cluster (8 intel-cores per node, GROMACS compiled with icc 11.1, all run through mvapich2): I have a molecule (protein 498aa, solvated or in vacuum I get the same problem at any box shape), wh

Re: [gmx-users] Constraints and ligands

P.R.Anand Narayanan wrote: Dear users, I just have 2 queries 1) Is it safe to use "united atoms" constraint for positional restraining and md simulation of an enzyme docked to the substrate? if yes, what is the KEYWORD to be typed in the mdp file and in what way is it simpler than the "all-bon

Re: [gmx-users] NAN in g_anaeig -proj

Hi Alex, Sorry for not replying earlier. Still haven't had time to do checks myself. But have you already tried to see what happens if you only request projections?: g_anaeig_d -v sss_1000_eigenvec.trr -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -first 1 -last 1 -n sss.ndx -proj Cheers, Tsjerk 2

[gmx-users] Solvating a CG system

Hi ALL, I have a CG protein in a CG lipid bilayer. I have packed the lipids around the protein using InflateGRO, following Justin's tutorial. Now I want to solvate it with CG waters. In all-atom we need to set a higher value for VanderWaal's radii for C in vdwradii.dat file. What should it be like

[gmx-users] How to calculate the lifetime of one hydrogen bond

Dear all, I want to calculate the lifetime of one hydrogen bond. I used g_hbond to do this. Here is the out put: Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward-0.001 -175

Re: [gmx-users] How to calculate the lifetime of one hydrogen bond

Dechang Li wrote: Dear all, I want to calculate the lifetime of one hydrogen bond. I used g_hbond to do this. Here is the out put: Hydrogen bond thermodynamics at T = 298.15 K -- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward

[gmx-users] Shear viscosity

Hi all, I am trying to master the art of shear viscosity calculation using "g_energy -vis". Plotting the first column in visco.xvg over time, the nearly straight line is obtained. Is it OK? How can one get the viscosity value from these data? My simulation details for this task are: NVT, 298K, shi

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Mark, I will test, but please tell me: do you think MPI linking problem could lead to problems with some dynamics and not with others as happens to me? and also note that all my test where made with mvapich2 (even that with one core). Please justin, what do you think about? Thanks Daniel 2009/10

Re: [gmx-users] Solvating a CG system

Anirban Ghosh wrote: Hi ALL, I have a CG protein in a CG lipid bilayer. I have packed the lipids around the protein using InflateGRO, following Justin's tutorial. Now I want to solvate it with CG waters. In all-atom we need to set a higher value for VanderWaal's radii for C in vdwradii.dat

Re: [gmx-users] user defined potential function for 1-4 interaction

Hi Berk: Thanks for your eply. I guess I would supply two column in the table for the bond type 9 [r(nm) and W(kJ/mol) ]. In that case (according to the user manual) what is the significance of k? how k will come into the calculation? If I select "constraints = all bond" will that affect bond

[gmx-users] Problem with CGMD

Hi ALL, Thanks Justin for your reply. Now after solvating my CG system of protein in lipid bilayer, I did EM and the final energy values were reasonable. But while running MD I am getting the following error: --- Fata

Re: [gmx-users] Problem with CGMD

Anirban Ghosh wrote: Hi ALL, Thanks Justin for your reply. Now after solvating my CG system of protein in lipid bilayer, I did EM and the final energy values were reasonable. But while running MD I am getting the following error:

Re: [gmx-users] Problem with CGMD

Hello Justin, Thanx for the reply I tried with dt=0.02 and also with dt=0.01. but still its crashing. It is crashing in the very first step. So nothings there in trr file. Are the options given in the MDP file correct? Actually my EM ran quite well. Please advice. Regards, Anirban On Fri, Oct 3

Re: [gmx-users] Problem with CGMD

Anirban Ghosh wrote: Hello Justin, Thanx for the reply I tried with dt=0.02 and also with dt=0.01. but still its crashing. It is crashing in the very first step. So nothings there in trr file. Are the options given in the MDP file correct? Actually my EM ran quite well. Please advice. If

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Daniel Adriano Silva M wrote: Mark, I will test, but please tell me: do you think MPI linking problem could lead to problems with some dynamics and not with others as happens to me? and also note that all my test where made with mvapich2 (even that with one core). Please justin, what do you thin

[gmx-users] Re: NAN in g_anaeig -proj

Hi Tsjerk! That is where I encountered NANs problem (except it was 10 eigenvectos, but for 1 NANs appears as well). I used -over option to check eigenvectors only. Now it seems for me that it is a bug and not my stupid typing mistake. What can really help in this case (IMHO!) is my problem

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Mark, Thank you!!! It was non directly MPI, since I tried the fresh installation with intel and gcc but none worked, then i realized that my compilation of FFTW could be the problem (compiled with icc 11), then I recompiled FFTW with gcc and linking to this new fftw3.2.2 I recompiled gromacs booth

Re: [gmx-users] Re: NAN in g_anaeig -proj

Hi Alex, Unfortunately I don't have time to dig into that now. It might indeed be a bug though and you might want to consider file a bugzilla report: http://bugzilla.gromacs.org That will put it on the table of the developers. Cheers, Tsjerk 2009/10/30 alexander yakovenko : > Hi Tsjerk! > That

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Daniel Adriano Silva M wrote: Mark, Thank you!!! It was non directly MPI, since I tried the fresh installation with intel and gcc but none worked, then i realized that my compilation of FFTW could be the problem (compiled with icc 11), then I recompiled FFTW with gcc and linking to this new fftw

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Mark, Then I will try with other versions, check gmx-tests and not mix compilers, thank you much by your help. Last question, I am afraid to ask, but I have some simulations that were ran with this setup, energy, temp, and pressure looks good on all, and it ran by pretty long time (several ns) wit

Re: [gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

Daniel Adriano Silva M wrote: Mark, Then I will try with other versions, check gmx-tests and not mix compilers, thank you much by your help. Last question, I am afraid to ask, but I have some simulations that were ran with this setup, energy, temp, and pressure looks good on all, and it ran by p

Re: [gmx-users] Setting up an infinitely hard wall

Hi Berk, I am mailing about the issue of setting up infinite potential well. I now want to simplify the task of inversing the velocity and mirroring the particle by the following procedure. If a particle is found in z wrote: > Hi, > > If you have a wall potential, you can reweight the configura