On 05/03/11, Kavyashree M wrote:
>
>
> On Sat, Mar 5, 2011 at 12:22 AM, Justin A. Lemkul wrote:
>
> >
> >
> >
> >
> >
> >
> >
> > It is difficult to say for certain how OPLS should be used with MD, since
> > it was originally designed for different software doing MC simulations. I
On Sat, Mar 5, 2011 at 12:22 AM, Justin A. Lemkul wrote:
>
> It is difficult to say for certain how OPLS should be used with MD, since
> it was originally designed for different software doing MC simulations. I
> commonly see rlist=rcoulomb=rvdw=1.0 with vdwtype = cutoff and coulombtype =
> PME
On 05/03/11, Sai Pooja wrote:
> Hi,
>
>
>
> In Manual 4.5.3, the potential for dihedral restraints is the following:
>
>
>
> Phi* = (Phi - Phi0)MOD 2Pi
>
>
>
> Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral.
> And the MOD2Pi, I assume, ensures a differen
On 05/03/11, "Justin A. Lemkul" wrote:
>
>
> Moeed wrote:
> >Hello,
> >
> >I am attempting to increase the density using NPT. As I increase the
> >pressure to compress the system after some steps simulation crashes. I
> >thought maybe its becasue I am compressing too fast but even when I ta
On 05/03/11, jonathan wrote:
> I previously supposed that the number of lipids selected was constant to
> simplify the problem.
>
> The distance criteria gives a different number of lipids for each frame.
> To end up with a constant number of atoms in the output trajectory,
> each lipid select
Hi,
In Manual 4.5.3, the potential for dihedral restraints is the following:
Phi* = (Phi - Phi0)MOD 2Pi
Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral.
And the MOD2Pi, I assume, ensures a difference <2Pi.
The Potential is: V=0.5*K*(Phi* - Phi0 -deltaPhi)**2
Kavyashree M wrote:
Dear gromacs users,
1. When one is using OPLSAA force field for simulation a protein of say
100aa to 250aa long protein, TIP4P water model in gromacs 4.5.3
what are the values of cut offs to be used ie., rcoloumb, rvdw,
rvdw-switch and rlist? I have gone through the m
Chih-Ying Lin wrote:
Hi
I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s)
But, the experimental data is around 1x1e-6 (cm2/s).
How could I explain for this discrepency?
If the simulation is based off of a simulation of a single lysozyme protein in
water, I'd be a
Justin A. Lemkul wrote:
Moeed wrote:
Hello Justin,
Thanks.
1- I changed the setting below because of the note I used to get:
NOTE 1 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
Dear gromacs users,
1. When one is using OPLSAA force field for simulation a protein of say
100aa to 250aa long protein, TIP4P water model in gromacs 4.5.3
what are the values of cut offs to be used ie., rcoloumb, rvdw,
rvdw-switch and rlist? I have gone through the manual and papers and
t
Dear gromacs users,
1. When one is using OPLSAA force field for simulation a protein of say
100aa to 250aa long protein, TIP4P water model in gromacs 4.5.3
what are the values of cut offs to be used ie., rcoloumb, rvdw,
rvdw-switch and rlist? I have gone through the manual and papers and
t
Hi
I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s)
But, the experimental data is around 1x1e-6 (cm2/s).
How could I explain for this discrepency?
Thank you
Lin
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Please
Hello,
I want to know if it is possible to use "mdrun-gpu" with the command
"-multi", meaning to use GPUs using paralell simulation.
When I used it (mdrun-gpu -multi 2 -replex 2 ), it appears me an error shown
bellow
* Fatal error:
This binary is compiled without MPI support, can not do multiple
si
Joanne Martin wrote:
Thanks Justin,
I think I have the restraints section sorted...
However, once all of the dihedrals are obtained from the MDs, I would
like to do a WHAM analysis, of the reaction pathway.
As I have to run each conformation as a separate MD in order to obtain
all di
Moeed wrote:
Hello Justin,
Thanks.
1- I changed the setting below because of the note I used to get:
NOTE 1 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance,
Hi João
I thought that the meaning of "epot" is the one you point out in your
mail. So, I'm also a surprised about your test.
The first thing that came to me mind is on the way you calculate the
energy with a "single" steepest descent step. In your mdp file, did
you use "nsteps=1" or "nst
Hello Justin,
Thanks.
1- I changed the setting below because of the note I used to get:
NOTE 1 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-
Thanks Justin,
I think I have the restraints section sorted...
However, once all of the dihedrals are obtained from the MDs, I would like
to do a WHAM analysis, of the reaction pathway.
As I have to run each conformation as a separate MD in order to obtain all
dihedral conformations, how c
Moeed wrote:
Hello,
I am attempting to increase the density using NPT. As I increase the
pressure to compress the system after some steps simulation crashes. I
thought maybe its becasue I am compressing too fast but even when I take
a stepwise approach to compress gradually the same error c
Hello,
I am attempting to increase the density using NPT. As I increase the
pressure to compress the system after some steps simulation crashes. I
thought maybe its becasue I am compressing too fast but even when I take a
stepwise approach to compress gradually the same error comes up. The density
I previously supposed that the number of lipids selected was constant to
simplify the problem.
The distance criteria gives a different number of lipids for each frame.
To end up with a constant number of atoms in the output trajectory,
each lipid selected in a frame is written in a separate outp
Joanne Martin wrote:
Hi Justin, thanks so much for the swift reply.
With regards to the mdp setting
> The proper setting for the "dihre" keyword is either "yes" or "no."
How to I specify which dihedral I want to restrain and the force
constant which I want to apply to it??
That's contr
Hi Justin, thanks so much for the swift reply.
With regards to the mdp setting
> The proper setting for the "dihre" keyword is either "yes" or "no."
How to I specify which dihedral I want to restrain and the force constant
which I want to apply to it??
Regards,
Joanne
On Fri, Mar 4, 2011 at 1:
Hello,
I am calculating vibrational spectra by calculating the Fourier transform
of dipole moment correlation function. I have fortran code for the
calculation of the Fourier transform autocorrelation function.
For better spectra I want to calculate the dipole autocorrelation function
at eash 1fs.
Joanne Martin wrote:
Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs
version 4.04.
I have read through all posts on the mailing list regarding this query,
and although Chris Neale did explain how to set the restraints for
Gromacs 3, these options are now obsolete for 4.04...
Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version
4.04.
I have read through all posts on the mailing list regarding this query, and
although Chris Neale did explain how to set the restraints for Gromacs 3,
these options are now obsolete for 4.04 I get the followi
On 04/03/11, jonathan wrote:
> Indeed, to be more specific, I would like to run a g_covar analysis on
> lipid acyl chains that are within a certain distance to a protein.
> Since the trajectories are quite long (+10K frames), splitting each
> frame to separate files, and then isolating the sele
Indeed, to be more specific, I would like to run a g_covar analysis on
lipid acyl chains that are within a certain distance to a protein.
Since the trajectories are quite long (+10K frames), splitting each
frame to separate files, and then isolating the selection would require
a lot of time.
I can
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