[gmx-users] what is the eigenvalue unit in Gromacs?

Dear all, I used g_nmeig to diagonalize the Hessian matrix, that I got the eigenvalues. However, I found that in the file 'eigenval.xvg' the unit of the eigenvalues are Eigenvalue [Gromacs units]. What is the '[Gromacs units]'? -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] question about how to install g_tune_pme

Hi Yi, the most convenient way in my opinion is to copy the Makefile.arch from the already installed gromacs-4.0.7 version and copy it into the directory where g_tune_pme.c is. Rename Makefile.arch to Makefile and inside it exchange the three occurences of template by g_tune_pme. Type make and

[gmx-users] pressure scaling more than 1%

Hi all, my simulation runs well for the first 70 steps with a step size of 0.001ps and when I get the warning that the pressure scaling is more than 1% every 1 step or so. So, is my tau_p of 0.2 to small or is the equillibration not done well enough. I am simulating a small peptide in

Re: [gmx-users] g_rmsf -res

Hi Tsjerk, thank you for your answer. Actually, for the initial structure, I took the values of the B factor, and calculated the mean square displacement per atom. This is what I meant by saying RMSF of initial structure. Anyway, thanks for the explanation. But I have another question: I need to

Re: [gmx-users] g_rmsf -res

Hi, yes it can be done with g_covar, but such an average structure is often of little physical significace. Imagine for instance the acerage structure of a rotating methyle group (it's a bunch of atoms on a line). Erik Carla Jamous skrev: Hi Tsjerk, thank you for your answer. Actually,

Re: [gmx-users] g_rmsf -res

Please does anyone know how is calculated the B factor in gromacs? What is the formula that gives the B factor with the average coordinates with g_rmsf? Carla On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund er...@xray.bmc.uu.sewrote: Hi, yes it can be done with g_covar, but such an average

[gmx-users] Coulomb (SR) problem

hello again I had a problem with a sim of some molecules in vacuum and a gmx-user told me to do a simulation only in one molecule just to see what gromacs calculates and what does not. My problem concerned the sum of all energies in the system. After i did the sim with one molecule i found out

Re: [gmx-users] Coulomb (SR) problem

On 2010-06-11 12.13, Thanasis Koukoulas wrote: hello again I had a problem with a sim of some molecules in vacuum and a gmx-user told me to do a simulation only in one molecule just to see what gromacs calculates and what does not. My problem concerned the sum of all energies in the system.

[gmx-users] restarting simulation

Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] restarting simulation

Gavin Melaugh wrote: Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s topol.tpr -cpi state.cpt -append If you're using default filenames, if

Re: [gmx-users] restarting simulation

Thanks guys XAvier Periole wrote: On Jun 11, 2010, at 3:30 PM, Gavin Melaugh wrote: Hi all For restarting a crashed simulation, do you have to use the -s topol.tpr in the command below. I have left it out and everything seems to be O.K. I'm just double checking though. mdrun -s

[gmx-users] top2psf.pl

Hi Trying to use top2psf.pl, as suggested Usage: top2psf.pl -i (topology filename) -o (output filename) but I get an error message saying invalid command name top2psf.pl Suggestions? Thanks Rabab -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] pressure scaling more than 1%

Sebastian Waltz wrote: Hi all, my simulation runs well for the first 70 steps with a step size of 0.001ps and when I get the warning that the pressure scaling is more than 1% every 1 step or so. So, is my tau_p of 0.2 to small or is the equillibration not done well enough. Possibly,

[gmx-users] combine position restraints and NPT equlibration in membrane

In God We Trust Hello Dear GMX users We would like to perform MD simulation of a protein in attendance of biomembrane (POPE). On the basis of Kalp tutorial, can we combine position restraints and NPT equlibration in one phase?. We attached NPT.mdp in this mail. Please guide us. Many

[gmx-users] Help! --- Permission denied (publickey, gssapi-with-mic, password).

Hi There, Please help me with this permission issue! Thanks. (Below are the input and output, followed by the information of my compiling procedure) #!/bin/csh -f #$ -cwd #$ -N gro.t.4 #$ -S /bin/tcsh #$ -l h_rt=120:00:00 #$ -e SGE.err #$ -o SGE.out #$ -pe mpich 4 mpirun -np 4 mdrun_mpi -s

[gmx-users] Disk Space

Dear Gromacs users, I am running an MD simulation but it looks to me that I am running out of disk space. This is my .mdp file ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout

[gmx-users] Selecting specific atoms to find average energy of

Hello, I ran an md simulation, and I have graphed the total average energy of the system by using g_energy to convert my binary .edr file into a text based file. What I want to do is to find the average energy between the solvent molecules, excluding the energy between the solute-solvent

[gmx-users] Disk Space

Dear Rob: To answer your question: just set up your run with nsteps for 5 ns, run mdrun, and then use tpbconv -until. A simpler option is to set it up to run 20 ns, but use -maxh to limit it to an amount of runtime that you pre-calculate to be similar to 5 ns of simulation. HOWEVER: You

Re: [gmx-users] GROMACS on CYGWIN

Also, use the 'nice' command to run gmx at high priority, and switch off CPU frequency scaling. For me, cygwin performance is pretty much the same as that on linux, which is to be expected since most of the code isn't dependent on system calls. Apparently, the only difference you should be able to

Re: [gmx-users] combine position restraints and NPT equlibration in membrane

Quoting Mahnam mah...@ibb.ut.ac.ir: In God We Trust Hello Dear GMX users We would like to perform MD simulation of a protein in attendance of biomembrane (POPE). On the basis of Kalp tutorial, can we combine position restraints and NPT equlibration in one phase?. We attached NPT.mdp in

Re: [gmx-users] Selecting specific atoms to find average energy of

Quoting Jennifer Casey jrcase...@gmail.com: Hello, I ran an md simulation, and I have graphed the total average energy of the system by using g_energy to convert my binary .edr file into a text based file. What I want to do is to find the average energy between the solvent molecules,