Hi all,
I am trying to simulate a small organic molecule (42 atoms with 18
hydrogens among them) in water (SPCE). The force field was generated
with X2TOP utility using GROMOS96 force field. All bonds, pairs,
angles, dihedrals, etc are OK and the system runs OK but sometimes it
craches producing
Hello,
I'm trying to do constrained simulations of a system consisting of two
solvated proteins separated at a given distance. Inside the box there are
also
around 14.000 water molecules. At the bottom there is the .pdo
file (I'm using gromacs 3.3.3).
However, it seems as it does not work. At
Hi.
Though not a GROMACS user, I always read the very interesting topics of
the mailing list. In this case I could maybe even help :) There is some
info about building nanotubes in the GROMACS wiki/mailinglist and some
nice papers about CNTs made with GROMACS by a someone called Johnson (if
I
*Hi
**
**after energy minimization step, how can be understand that obtained
**structure is in global or local minimum?
**
**
*
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shahab shariati wrote:
/Hi
//
//after energy minimization step, how can be understand that obtained
//structure is in global or local minimum?
//
//
/
This identical question was posted just a few days ago and received an answer
then:
Hi
How pdb file for CNT is made?
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This question came up a few weeks ago.
The simple answer is, you can be pretty sure you're at the bottom of
some potential energy surface but you can't know if you're at a local
or global minimum.
However, if you are using an experimentally determined protein
structure, and the structure
Please provide actual gromacs output and tell us where it is from. I
know it's sad, but not all of us can recall what the gromacs 3.3.3
.pdo file format looked like. So please include a sufficiently large
portion of the file to help us recall. If, on the other hand, these
values that you
Sounds like a bubble. Do some NpT equilibration by adding pressure
coupling. That's going to be difficult with your freeze groups though.
Basically, you need to find a way to get the correct solution density
between the graphite layers.
-- original message --
Hi all,
Is there anyone who
1. Is your system is properly minimized
2. If you take the output from a 500 ps run with 0.25 fs timestep and
start a 1 fs timestep run, is that new run stable?
3. What are atoms 62 and 80?
**4. Why is there a 1-4 between atoms 62 and 80 if you have only water
and a 42 atom solute?
5. What
Dear Giuseppe:
I don't think your method of showing the change is very good since it
introduces unnecessary variables (e.g. did you use the correct files
for the second run).
What I am looking for is raw -pd pull.pdo data from the first run. I
found no such file in the body of the email
Chris:
you're right man, let me be more concise.
Here there is the execution line I used:
mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c
output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 *
As for the pull.ppa file, here you go:
; GENERAL
verbose
Hi Chris,
1. Is your system is properly minimized
Of course, it is, based on the energy values.
2. If you take the output from a 500 ps run with 0.25 fs timestep and
start a 1 fs timestep run, is that new run stable?
Unfortunately the new run also crashes. The crash may be at the very
end
Dear Giuseppe:
*** What I am looking for is raw -pd pull.pdo data from the first run. ***
It looks like you did not define a name for -pd:
mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c
output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 *
so based on
Got it!
Ok, first lines:
# CONSTRAINT3.0
# Component selection: 1 1 1
# nSkip 1
# Ref. Group 'protein_b'
# Nr. of pull groups 1
# Group 1 'protein_a' Pos. 3.099513 2.982803 3.377482
#
0.00-787.501479
0.002000-271.159600
0.004000
1. Is your system is properly minimized
Of course, it is, based on the energy values.
Don't be so sure! Although since your 0.25 fs timestep -- 1 fs
timestep transition crashes you are likely correct here.
**4. Why is there a 1-4 between atoms 62 and 80 if you have only water
and a 42
Dear Giuseppe:
OK, those are the forces. They seem pretty huge and massively
fluctuating, although I use umbrella sampling myself so this might be
quite normal for constraint sampling (something for you to look into).
The only thing that comes to mind is that your running up against a
There's your problem (although in a different manner than I thought).
If you have, for example, 3 solutes, then you should have
[ molecules ]
CIP 3
-NOT-
[ molecules ]
CIP 1
Of course, the number of moleules in .top and .gro files coincides.
Otherwise, one would have had immediate
Vitaly V. Chaban wrote:
There's your problem (although in a different manner than I thought).
If you have, for example, 3 solutes, then you should have
[ molecules ]
CIP 3
-NOT-
[ molecules ]
CIP 1
Of course, the number of moleules in .top and .gro files coincides.
Otherwise, one would
Justin,
All the directives are correct. Chris just mistyped saying
[ molecules ]
CIP 3
instead of
[ moleculetype ]
CIP 3
that I orginally send him.
He can't know how many CIPs I have in my system because I didn't send
him this section. :)
Vitaly
On Sun, Jan 24, 2010 at 8:39
Vitaly V. Chaban wrote:
Justin,
All the directives are correct. Chris just mistyped saying
[ molecules ]
CIP 3
instead of
[ moleculetype ]
CIP 3
that I orginally send him.
He can't know how many CIPs I have in my system because I didn't send
him this section. :)
You said
Dear Vitaly:
Justin raises the point well, so that should be addressed first. If,
however, you still have problems then there's the only thing that I
can think of:
1. put a single solute in a large vacuum box and use the sd
integrator. Can you reproduce the problem?
2. Remove the
Dear Chris:
I don't think it is something related to pbc because my solutes are well
inside the simulation box (as I told you before I visualize them via a movie
while the simulation proceeds).
Nor it is something related to the barostat because I saw that warning
and in order to try to see it
All the directives are correct. Chris just mistyped saying
[ molecules ]
CIP 3
instead of
[ moleculetype ]
CIP 3
that I orginally send him.
Not true. I meant exactly what I typed. I am referring to the section
that occurs at the end of your .top file:
It sometimes looks like
You said before:
5. What does your .top look like? (does it list the organic molecule
only once in the [ molecules ] section?)
Only once.
OK. We misunderstood one another. I meant CIP is mentioned only once
= one string with CIP molecules number. So this entry was not really
Dear Giuseppe:
This is a pretty good example of how it can be useful to completely
describe what you are doing at first posting. What you mention could
easily be a problem for a couple of reasons:
1. The manual indicates that you may need more than one shake
iteration in this case (or at
Dear Chris -
1. put a single solute in a large vacuum box and use the sd
integrator. Can you reproduce the problem?
No problem in vacuo found.
2. Remove the dihedral parameters entirely. Can you reproduce the problem?
The problem appeared between carbon and hydrogen 1-4 atoms... Would
you
Dear Vitaly:
1. No problem at all in vacuo? That with a 1 fs timestep and the sd
integrator? Strange then that your molecule is ok and the water is ok,
but they are unstable together. Perhaps your'e not getting any LJ
interactions (or not correct ones) between your solute and water? That's
Hi,I want to simulate a finite CNT and CNT is flexible .but during time
simulation of nanotube is outside the simulation box and again into the box
is return ,and finally , in the end simulation time,half of CNT remains
outside the box.please guid me to solve this problem . thanks
--
gmx-users
Hi,
Thanks a lot for the suggestion! NPT does is difficult with the frozen
graphite layers. On the other hand, I have also done another simulation
using the implicit graphite wall with the same polymer solution
(composition and system volume). These implicit wall systems seems good,
at least
neo lotus wrote:
Hi,I want to simulate a finite CNT and CNT is flexible .but during time
simulation of nanotube is outside the simulation box and again into the
box is return ,and finally , in the end simulation time,half of CNT
remains outside the box.please guid me to solve this problem
Hello,
I am running rdf simulations, and I tried running simple methane
using OPLS-AA force-field for 100ns. I was hoping to get a smoother
curve for such a small molecule in 100ns. Could someone please look
over my mdp parameters and suggest if I am missing something.
Thanks.
Nisha
Dear Nisha:
I looked only at the rdf, and it seems entirely reasonable. 100 ns may
be a long simulation, but you only have 1 methane and that's what
leads to you having much less data than if you were for instance
looking at water-water rdfs.
If you want it to look smoother, then use
I suggest you first can run a system with only polymer solution in NPT
ensemble. After a suitable density is reached, then you can add two
graphite sheets into the equilibrated system, please set the distance
between graphite and solution carefully (or trial error).
Best wishes,
Zhongqiao
Hi,
Hi All,
I was trying *GROMACS Tutorial for Drug – Enzyme Complex* by *John E.
Kerrigan* over one docked complex in following way.
I generated topology and gromacs co-ordinates for ligand and cofactor
successfully using PRODRG beta.
Protein file is processed through pdb2gmax_d and resulted .gro
Hi Vivek,
Now when I am processing the modified .gro file to generate box, the ligand
and cofactor are going away from the protein molecule and I am not able to
analyze the complex.
Gradually going away, or suddenly jumping?
In the latter case, read up on periodic boundary conditions.
Hi Pawan,
Check which shell you're actually running (probably bash), and source
the shell specific GMXRC file (GMXRC.bash).
Cheers,
Tsjerk
On Mon, Jan 25, 2010 at 8:19 AM, pawan raghav pwnr...@gmail.com wrote:
Dear Justin,
I have some problem regarding GMXRC execution, I got an error while
- Original Message -
From: pawan raghav pwnr...@gmail.com
Date: Monday, January 25, 2010 18:21
Subject: [gmx-users] GMXRC Problem
To: gmx-users@gromacs.org
Dear Justin,
I have some problem regarding GMXRC execution, I got an error while using
gromacs-4.0.7 on windows vista using
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