- Original Message -
From: pawan raghav
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 cygwin i.e.
>
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 wrote:
> Dear Justin,
>
> I have some problem regarding GMXRC execution, I got an error while using
> gromacs
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.
Tsj
Dear Justin,
I have some problem regarding GMXRC execution, I got an error while using
gromacs-4.0.7 on windows vista using cygwin i.e.
/usr/local/bin/GMXRC: line 35: return: can only 'return' from a function or
sourced script.
/usr/local/bin/GMXRC: line 44:CSH::command not found
/cygdrive/c/Gro
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 a
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,
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 larg
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
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 .
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
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 m
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
wh
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 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
> 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
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 this
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 wo
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 dihedra
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 befo
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:
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 hav
>
> 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 imme
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
pbc
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 at
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
0.004000-1147.35
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
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
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
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
Hi Chris,
the pdo file was attached at the bottom of my previous e-mail. As for
the output, you may read the information about the COMs in the md.log
file. Here there is an extended portion of it at the beginning of the
simulation:
**
neo lotus wrote:
Hi
How pdb file for CNT is made?
Have a look at the following:
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Bi
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 do
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 c
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 pl
Hi all,
Is there anyone who can give me some suggestions?
My system is composed of some polymer chains and waters. The density of
the solution is about 1g/cm^3. Then I added two explicit grahpite layers
(resname=WAL) at the bottom and top of the solution, which are both
freezed in three dimen
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
Hi
How pdb file for CNT is made?
--
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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:
http://lists.gromacs.org/pipermail/gmx-users/2010-
*Hi
**
**after energy minimization step, how can be understand that obtained
**structure is in global or local minimum?
**
**
*
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before p
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 reme
> Hi,I want to simulate gas adsorption on finite CNT. Does CNT be flexible
> or rigid? which is better? thanks
In your situation, it depends on gas pressure. The bigger the pressure
is - the less is the difference between flexible and rigid nanotube
force fields. Please also look through the pa
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 the
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 s
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