[gmx-users] g_covar with individual masses

Dear Gromacs users, I want to calculate the covariance matrix of the center of mass coordinates of non standard residues. Since I want to do it mass weighted I need to give the center of mass masses. From which file does g_covar read the masses? Thanks a lot Sebastian -- gmx-users mailing li

[gmx-users] DMSO compressibility

Hi all, can someone tell which compressibility should be used for DMSO at 300K? Thanks a lot Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] coinstraint bond length changes

Hi all, I constrained in the .top file some bonds [ constraints ] ;ai aj typedistance 4041 2 0.1430 4748 2 0.1430 5455 2 0.1430 6162 2 0.1430 After running the simulation for 5ns I get a bond length of 0.23(out

[gmx-users] Forces on atom which is shifted out of the minimum

Hi all together, I need to calculate the first derivative of the force or the second derivative of the potential. Therefore I need the force on an atom which is shifted out of the minimum along the constrained bond direction for each time step. There in the Gromacs code is the force actually calcu

[gmx-users] Instantenous Hessian Matrix

Hi all, is there a way to get the hessian matrix for each time step for which I also print out the trr? Or do I have to run normal mode analysis for each configuration? Thanks a lot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

[gmx-users] which flag for the force

Hi all, I want to get the forces out of the .trr file using the template.c given. My question is what flag should I use in the last loop to get the force f? I don't find anything in the directory which is given in the example. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lis

[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 CHCl

[gmx-users] constraints bond length vari by 10%

Hi all, I added constraints on some bonds in my system by adding [ constraints ] ;ai aj typedistance 40 41 1 0.1230 47 48 1 0.1230 54 55 1 0.1230 61 62 1 0.1230 to me top file (CO double bonds) and in the mdp file co

Re: [gmx-users] constraints bond length vari by 10%

On Wed, 16 Jun 2010 09:05:20 +1000 Mark Abraham wrote: > > > - Original Message - > From: Sebastian Waltz > > Date: Tuesday, June 15, 2010 22:09 > Subject: [gmx-users] constraints bond length vari by 10% > To: gmx-users@gromacs.org > > > Hi all,

Re: [gmx-users] constraints bond length vari by 10%

- Original Message - > From: Sebastian Waltz > > Date: Thursday, June 17, 2010 2:23 > Subject: Re: [gmx-users] constraints bond length vari by > 10% > To: Discussion list for GROMACS users > > > > Hi Mark, > > > > what I have written in the .to

Re: [gmx-users] constraints bond length vari by 10%

ke to know what does the shake_tol means. Thanks On Fri, 18 Jun 2010 09:37:36 +1000 Mark Abraham wrote: > > > - Original Message - > From: Sebastian Waltz > > Date: Thursday, June 17, 2010 18:59 > Subject: Re: [gmx-users] constraints bond length vari by >

[gmx-users] get the mass having the atom type

Hi all, I am using the template.c file to make some individual analyses. Using top.atoms.atomtype[i] I can get the information of the atom type of atom i. Is it then possible to use this information to get the mass of this specific atom? Thanks a lot -- gmx-users mailing listgmx-users@groma

Re: [gmx-users] Re: Problem of reading the atom'force from trr file using template.c

Hi Chuan, in the template.c file is in the beginning the flag initialized: intflags = TRX_READ_X; If you want to read out the forces you have to change this to, as: intflags = TRX_READ_F; in addition to changing fr.x to fr.f. Basti On Wed, 23 Jun 2010 20:00:27 +0800 聂雪川 wr

[gmx-users] different ref_t

I try to simulate a small peptide in CHCl3 there the peptide is couplet to a heat bath at a different temperature: tcoupl = nose-hoover tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.01 0.01 ref_t = 220 300 If I do so the temperature of the C