Quoting pawan raghav :
> I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water
> model. Is it likely mean that position restrained dynamics is not required.
As soon as you introduce a protein or anything else, this is no longer true.
> If we are not intersted in position restr
I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water
model. Is it likely mean that position restrained dynamics is not required.
If we are not intersted in position restrained dynamics then what are the
criteria for system needed.
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Pawan
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Thank you for the discussion. I am basically having a similar problem:
position restraining (PR) 2 plates in NPT and the system blow up
(posted here:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055975.html).
I will try to use smaller time step to see whether the situation
becomes be
On 21/11/2010 9:09 PM, pawan raghav wrote:
Thank mark for comments, but I have check the structure after energy
minimization through ramachandran plot and found 82% residues were
lies in core region. After performed position restrained dynamics it
reduced to 52% in core region also 1 bad contac
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Hello,
I haven't read the mails before, but as long as you are not in
equilibrium I do not think that PR coupling is the best way to go.
Furthermore PR is very sensitive to constraints and the time step, so
perhaps 2fs is too large. Try to perform a s
Thank mark for comments, but I have check the structure after energy
minimization through ramachandran plot and found 82% residues were lies in
core region. After performed position restrained dynamics it reduced to 52%
in core region also 1 bad contact was found. I have taken SPC water model
then
On 1/9/10 11:25 AM, chris.ne...@utoronto.ca wrote:
Hi Justin,
I just double checked and certainly the confout.gro from my EM run in
parallel with domain decomposition in mdrun is broken over periodic
boundaries.
I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp file
Tha
Hi Justin,
I just double checked and certainly the confout.gro from my EM run in
parallel with domain decomposition in mdrun is broken over periodic
boundaries.
I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp file
gpc-f101n084-$ cat em_pos.mdp
define=-DPOSRES_INDO
con
On 1/9/10 10:49 AM, chris.ne...@utoronto.ca wrote:
Dear Sunny,
I replied a while ago, but it seems to have not made it to the list.
When using inflategro with gromacs3, you can run cycles like this:
1. inflategro.pl
2. mdrun (EM)
3. goto 1
When running with gromacs4, however, you must run cy
Dear Sunny,
I replied a while ago, but it seems to have not made it to the list.
When using inflategro with gromacs3, you can run cycles like this:
1. inflategro.pl
2. mdrun (EM)
3. goto 1
When running with gromacs4, however, you must run cycles like this:
1. inflategro.pl
2. mdrun (EM)
3.
On 1/8/10 7:30 PM, sunny mishra wrote:
Hi All,
I am trying to insert coarse grained protein to coarse grained lipid. My
protein is CG 1SU4 and lipid is CG DPPC. I can make a big hole and pack
lipids around the protein using INFLATEGRO script. But when I do the EM
of the system the minimized sy
Hi All,
I am trying to insert coarse grained protein to coarse grained lipid. My
protein is CG 1SU4 and lipid is CG DPPC. I can make a big hole and pack
lipids around the protein using INFLATEGRO script. But when I do the EM of
the system the minimized system comes out at a very bad shape. I have
Hi
we are simulating a protein of 260 a.a length which is a trimer...How does
the MDRUN time during the PR affects the Full Dynamics results???
Lucky
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On Sun, 26 Oct 2008 17:12:26 +0330
"hazizian" <[EMAIL PROTECTED]> wrote:
Hi gromacs users
I have done Position restrain for 50 ps.
after it had finished, I checked the rmsd for confident that rms reached to
it's equilibrate mode. When I check it by g_rms command and select system
subgroup, I
Hi gromacs users
I have done Position restrain for 50 ps.
after it had finished, I checked the rmsd for confident that rms reached to
it's equilibrate mode. When I check it by g_rms command and select system
subgroup, I find that it had not reached to equilibria, but after I check
It by p
minnale wrote:
Hi all,
I have two doubts on PR, may be these are trivial to you.
1.According to Gromacs procedure(from Gromacs tutorial) the sequential
steps are (a)Energy minimisation (b)Position restrain with force
constant descendant manner and finally (c)production. Here my doubt
tha
Hi all,
I have two doubts on PR, may be these are trivial to you.
1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps
are (a)Energy minimisation (b)Position restrain with force constant descendant
manner and finally (c)production. Here my doubt that, is it require to
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