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
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Hi all,
can someone tell which compressibility should be used for
DMSO at 300K?
Thanks a lot
Sebastian
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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
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
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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
to know what does the shake_tol means.
Thanks
On Fri, 18 Jun 2010 09:37:36 +1000
Mark Abraham mark.abra...@anu.edu.au wrote:
- Original Message -
From: Sebastian Waltz
sebastian.wa...@physik.uni-freiburg.de
Date: Thursday, June 17, 2010 18:59
Subject: Re: [gmx-users] constraints
:
- Original Message -
From: Sebastian Waltz
sebastian.wa...@physik.uni-freiburg.de
Date: Thursday, June 17, 2010 2:23
Subject: Re: [gmx-users] constraints bond length vari by
10%
To: Discussion list for GROMACS users
gmx-users@gromacs.org
Hi Mark,
what I have written
On Wed, 16 Jun 2010 09:05:20 +1000
Mark Abraham mark.abra...@anu.edu.au wrote:
- Original Message -
From: Sebastian Waltz
sebastian.wa...@physik.uni-freiburg.de
Date: Tuesday, June 15, 2010 22:09
Subject: [gmx-users] constraints bond length vari by 10%
To: gmx-users@gromacs.org
Hi
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
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
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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
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Please
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
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
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