Hi!
I have been running MD simulations on a 6 processors machine. I just got an
account on a cluster. A nvt stabilization takes about 8 hours on my 6
processors machine, but it takes about 12 hours on the cluster using 16
processors. It is my understanding that the idea of running in parallel is
t
Looking into the manual, i find under the 'energy monitor group':
'Mutual interactions between all energy monitor groups are compiled
during the simulation. This is done separately for Lennard-Jones and
Coulomb terms. In principle up to 256 groups could be defined, but that
would lead to 256x2
On 3/15/13 9:43 AM, Shima Arasteh wrote:
I also included the position restraints as follows in my top file:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "backbone_posre.itp"
#include "strong_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef
On 3/15/13 8:50 AM, Shima Arasteh wrote:
Dear users,
Although I put the position restraints on backbone, I get RMSD around 0.2 nm.
Is it usual?
No, 0.2 nm is very high. With position restraints, offhand I would think around
0.05 nm or less would be indicative of proper restraints.
Thi
On Fri, Mar 15, 2013 at 7:27 PM, Jeff Woodford <
jwoodf...@missouriwestern.edu> wrote:
> Hi all,
> I am attempting to simulate a system that has strong ionic character so I
> would like to treat the electrostatics and van der Waals interactions
> separately. For example I would like to include al
On 2013-03-15 15:31, Per Larsson wrote:
Hi
I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a
4.5.X-tpr file with dihedral restraints?
I'm unsuccessful in making them start.
To investigate further, I created a small dialanine peptide in vacuum, with a
dihedral restrai
On 2013-03-15 19:27, Jeff Woodford wrote:
Hi all,
I am attempting to simulate a system that has strong ionic character so I would
like to treat the electrostatics and van der Waals interactions separately.
For example I would like to include all pairs of atoms in the electrostatics
calculatio
That means the automatic download of FFTW did not succeed for some reason.
GROMACS is not going to compile an FFTW for you unless it's sure the FFTW
download was complete and the right file. Either do "make clean" and try
again, or follow the other build instructions to prepare a suitable FFTW
for
Hi all,
I am attempting to simulate a system that has strong ionic character so I would
like to treat the electrostatics and van der Waals interactions separately.
For example I would like to include all pairs of atoms in the electrostatics
calculation but I would like to exclude 1-2 and 1-3 ne
Dear all,
I'm receiving a "timesteps don't match" error, due to a wobble in the time
between steps for my xtc trajectory file. The source of the wobble is
mysterious.
I'm running gromacs-4.5.5 with plumed patches for a very long trajectory
using double precision code with a time step of 2fs and x
Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and
dirty installation I have this errors:
[ 1%] Performing download step (download, verify and extract) for 'gmxfftw'
-- downloading...
src='http://www.fftw.org/fftw-3.3.2.tar.gz'
dst='/home/biomedicina/gromacs/grom
Hi
I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a
4.5.X-tpr file with dihedral restraints?
I'm unsuccessful in making them start.
To investigate further, I created a small dialanine peptide in vacuum, with a
dihedral restraint.
Here's the details:
Making a 4.5.5
I also included the position restraints as follows in my top file:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "backbone_posre.itp"
#include "strong_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRE
#include "strong_posre.itp"
#include "b
Dear users,
Although I put the position restraints on backbone, I get RMSD around 0.2 nm.
Is it usual?
This deviation is just for a minimization step only. I' m on doubt about
keeping the backbone in a fix secondary structure.
I' d prefer to restraint the backbone completely. Is it possible?
A single frame proves very little. You should be looking at the trends in
(say) average values in observables relevant to what you're going to want
the simulation to sample. It's a bit of a dark art, however.
Mark
On Fri, Mar 15, 2013 at 11:02 AM, Abhishek Acharya wrote:
> Thanks for replying Ma
Thanks for replying Mark
So in that case, i presume a proper npt run should indicate all is
well with the system. Since there was nothing wrong in the output .gro
file of nvt and also the npt run was alright , should i go ahead with
the production run ?
Abhishek
What happens when you take a child
On Fri, Mar 15, 2013 at 9:28 AM, wrote:
> hi,
> I am trying to simulate a 50 residue protein in implicit water.Can anyone
> tell me that why we usually set the cuttoff to be 0.
>
See pbc = no in chapter 7.
> coulombtype = Cut-off
> vdwtype = Cut-off
> nstype = grid
> nstlist = 0
> rlist = 0
>
What happens when you take a children's swing in the playground, place it
in some crazy position and push it off in some random direction? The swing
will swing, but it won't look "proper" for a while. Apparently your initial
conditions are a bit crazy, e.g. some void next to your solute where a
sol
hi,
I am trying to simulate a 50 residue protein in implicit water.Can anyone
tell me that why we usually set the cuttoff to be 0.
coulombtype = Cut-off
vdwtype = Cut-off
nstype = grid
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0.
I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you exp
Dear Dallas
Thanks for your reply. I followed the way of you said to modify the
residue number in sequence. It generated a complete sturctural file
(conf.gro) without deleting the duplicate atoms. However, it denoted another
strange structure which contained many seperated residue
—(CH2-C
Dear Dallas
Thanks for your reply. I followed the way of you said to modify the
residue number in sequence. It generated a complete sturctural file
(conf.gro) without deleting the duplicate atoms. However, it denoted another
strange structure which contained many seperated residue
—(CH2-CF
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