Hi Manoj,
The error is clear. Check the settings referred to in your .mdp file and
modify them accordingly.
Cheers,
Tsjerk
On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in
wrote:
Dear All,
i'm geting below error while subjecting my system (Protein-ligand) for
equlibriation
Thanks Justin! I cant find so much details in the manual; there are only
general facts. does g_density give partial density?
On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote:
Hi Justin
The fact is I want to calculate water density in the system. If I select
group1: oxygen
ERROR 1 [file nvt.mdp]:
With coulombtype = PME-Switch, rcoulomb must be = rlist
On Tue, May 19, 2015 at 10:25 AM, manoj damale
manojaurangabad...@yahoo.co.in wrote:
what exactly i should modify
With Best Regards.
Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West
Hi Chris,
As far as I understand it, before GROMACS 5 the potential rather than the force
was switched off. Since GROMACS 5 you can choose between the two.
As for the settings to use with the CHARMM force field, the CHARMM package
itself (as Justin has said) uses force switching. However, in
Dear Gromacs Users,
I have the problem with generating the octahedron box. I always get the
rectangular box (using VMD)
When I searched on the gmx maillist, I saw some people met same problem.
Is problem is normal in gromacs?
After run simulation, I can display the trajectory on VMD by using the
Hi Tuong Vy,
An octahedral or dodecahedral box is pretty tricky. I have a Pymol script
for generating them, but it will probably require some more work...
Cheers,
Tsjerk
On May 19, 2015 13:18, Vy Phan phanvy120...@gmail.com wrote:
Dear Gromacs Users,
I have the problem with generating the
Dear all,
While generating RMSD plots of protein in presence of ligand, i am getting
a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost
stable.
Is it an acceptable RMSD?
What is the acceptable range for RMSD for structures?
--
*Let us all join hands to save our Mother
Please keep conversations on the mailing list. And please read the manual.
And note that the error is completely different this time.
Tsjerk
-- Forwarded message --
From: manoj damale manojaurangabad...@yahoo.co.in
Date: May 19, 2015 12:19
Subject: Re: [gmx-users] Gromacs Error
On 5/19/15 4:12 AM, mah maz wrote:
Thanks Justin! I cant find so much details in the manual; there are only
general facts. does g_density give partial density?
Read the first sentence of the help description :)
-Justin
On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote:
On 5/19/15 6:29 AM, Priya Das wrote:
Dear all,
While generating RMSD plots of protein in presence of ligand, i am getting
a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost
stable.
Is it an acceptable RMSD?
What is the acceptable range for RMSD for structures?
Ah, cool. I had misread that Chris was saying shift rather than switch in parts
of his previous email. Good to know that force switching can also be achieved
in GROMACS versions prior to 5.
Cheers
Tom
From:
Hi all,
I have some general doubts about the use of an itp file built by
some software. I am studying the dynamics of a DNA in presence of a
graphene sheet. I am using now the CHARMM27 force field and have obtained a
graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon
Hi everyone,
I never got a reply to my message but I figured out the problem by myself. Just
in case anyone else runs into a similar problem I thought I should explain what
was wrong and share the solution.
I was using a DMSO topology from the ATB that uses extra bonds to fix the
geometry
Dear all,
I am trying to compute the interaction energy between a small peptide
and water from a short MD simulation (54a7, reaction-field, Verlet, GPU,
gmx 5.04, 1 peptide, 3200 SOL molecules). I have specified SOL and
Protein as energy groups. Contrary to my expectations, LJ and Coul
energies
Hi,
You can easily generate position restraints files yourself - have a look at
one and learn about the column format from chapter 5. There is also gmx
genrestr to help with this - but read the documentation first.
Mark
On Tue, May 19, 2015 at 2:10 PM soumadwip ghosh soumadwipgh...@gmail.com
Hi
On Tue, May 19, 2015 at 5:35 AM Christopher Neale
chris.ne...@alum.utoronto.ca wrote:
Dear Justin:
Thank you for the suggestion. I don't use gromacs 5 because of things like
this: http://redmine.gromacs.org/issues/1603 that tend to pop up early in
a release series. Until I needed to run
Hi Tuong Vy,
No, it uses Pymol CGO to draw the cell. I think that won't work in VMD.
Cheers,
Tsjerk
On May 19, 2015 15:28, Vy Phan phanvy120...@gmail.com wrote:
Dear Tsjerk Wassenaar
Can I display it on the VMD ?
Thank a lot
Tuong Vy
2015-05-19 20:22 GMT+09:00 Tsjerk Wassenaar
On 5/19/15 10:15 AM, soumadwip ghosh wrote:
Thanks Mark for the prompt reply. I can probably make the posre files if
required now. But I would be relieved if someone sheds light on the first
question that if I already have an .itp file is is necessary to make an
entry for the atoms in the
Thank you so much for the suggestion.
Tuong Vy
2015-05-19 23:15 GMT+09:00 Mark Abraham mark.j.abra...@gmail.com:
Hi,
EM is implemented separately from MD, and since people rarely write enough
trajectory-frame coordinates from EM for I/O to be a serious issue, there's
no good reason to
On 5/19/15 11:19 AM, Andrew Bostick wrote:
Dear Tsjerk, Justin and Mark
Very thanks for your answers and guidance.
I installed gromacs 5.0.5. I used gmx pdb2gmx -f be_near.pdb -ignh -merge
all.
I want to have a link between two chains (CD atom of GLU residue from
chaim B and NZ atom of LYS
Dear Tsjerk, Justin and Mark
Very thanks for your answers and guidance.
I installed gromacs 5.0.5. I used gmx pdb2gmx -f be_near.pdb -ignh -merge
all.
I want to have a link between two chains (CD atom of GLU residue from
chaim B and NZ atom of LYS residue from chain E) to get isopeptide bond
Hi,
somewhat off-topic but I wonder why in your free energy protocol you
only vary the vdW and electrostatic lambdas. What about the others?
Your mutation also transforms bonded terms and masses.
One minor point is that your duplication of atomtypes (with i and m
prefixes) seems pretty
Hi,
mdrun doesn't see any problems, but if something else is reporting 25%
utilization then that probably means you have something else running on
your machine, which is a terrible idea for running mdrun. You should expect
some slowdown wrt to the non-free-energy version of the run - the
somewhat off-topic but I wonder why in your free energy protocol you
only vary the vdW and electrostatic lambdas. What about the others?
Your mutation also transforms bonded terms and masses.
Minor point - if you are taking the difference between two mutations (say,
with and without a
Dear Justin
Based on your answer (You don't want to be adding 2 HZ here, just one
since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file
LYS2 2
1 1 H N -C CA
1 4 HZ NZ CE CD
But, after pdb2gmx, I encountered with
WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file
On 5/19/15 12:12 PM, Hannes Loeffler wrote:
On Tue, 19 May 2015 12:03:41 -0400
Michael Shirts mrshi...@gmail.com wrote:
Yep, that's what I generally do. Almost all alchemical changes
involve a difference in two calculations (since the alchemical change
itself is unphysical). Even
On 5/19/15 1:15 PM, Priya Das wrote:
Yes Justin...i watched the dynamic structure carefully. As it is a
transmembrane protein it is stringently moving.
The dynamic movement of the structure seems fine.
I used the backbone of protein for calculating Rmsd.
Consider everything else I said.
I
On 5/19/15 2:45 PM, Andrew Bostick wrote:
Dear Justin
Based on your answer (You don't want to be adding 2 HZ here, just one
since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file
LYS2 2
1 1 H N -C CA
1 4 HZ NZ CE CD
But, after pdb2gmx, I encountered with
WARNING: atom HZ1
On Tue, 19 May 2015 17:48:17 +0200
Julian Zachmann frankjulian.zachm...@uab.cat wrote:
Concerning the changes of the atom types: the changes in the charges
are really small and the results will probably be the same if I would
not convert the whole ligand, just the 4 atoms which are changing.
On Tue, 19 May 2015 11:37:11 -0400
Michael Shirts mrshi...@gmail.com wrote:
somewhat off-topic but I wonder why in your free energy protocol you
only vary the vdW and electrostatic lambdas. What about the others?
Your mutation also transforms bonded terms and masses.
Minor point -
Hi everyone,
I try to compile GROMACS 5.0.5 on Fujitsu PRIMEHPC FX-10 with the command
from installation instruction page
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#linear-algebra-libraries
I use the Fujitsu compiler with the custom build toolchain as suggestion
from the
Hi,
I have used g_clustsize to count the number of molecules (they differ by
chain id) in the maximum populated cluster. Is it also possible to label
these molecules? i.e. to print chain ids of these molecules with time in
separate file?
Thanks in advance
--
Gromacs Users mailing list
* Please
Yes Justin...i watched the dynamic structure carefully. As it is a
transmembrane protein it is stringently moving.
The dynamic movement of the structure seems fine.
I used the backbone of protein for calculating Rmsd.
I also want to know the ligand stability, for it i need to check the least
Dear All,
I am new user of Gromacs and I am facing with a problem during a Tutorial
that until now It was not solved.
The following message appear: The switching range for PME-Switch should be
5% or less, energy conservation will be good anyhow, since ewald_rtol =
1e-05.
I would like
Hello Hannes,
As Michael said it is better to leave most things untouched and just change
VDW and LJ - at least this is what I have been reading so far.
Concerning the changes of the atom types: the changes in the charges are
really small and the results will probably be the same if I would not
As Michael said it is better to leave most things untouched and just change
VDW and LJ - at least this is what I have been reading so far.
Well, I didn't quite say this. Changes in the bonded terms do not entirely
cancel. Changes in masses do 100% cancel because of the seperability of
Yep, that's what I generally do. Almost all alchemical changes involve a
difference in two calculations (since the alchemical change itself is
unphysical). Even one-calculation solvation free energy calculations are
actually calculating the difference in free energy from liquid to vapor
state.
Concerning the changes of the atom types: the changes in the charges
are really small and the results will probably be the same if I would
not convert the whole ligand, just the 4 atoms which are changing.
However, as i had both ligands parametrised, I thought it would be a
good idea to
On Tue, 19 May 2015 12:03:41 -0400
Michael Shirts mrshi...@gmail.com wrote:
Yep, that's what I generally do. Almost all alchemical changes
involve a difference in two calculations (since the alchemical change
itself is unphysical). Even one-calculation solvation free energy
calculations are
Hi,
Thanks, sorry about that. We'll fix that for next release.
You can simply remove the call on line 472 of src/gromacs/mdlib/tpi.c
Mark
On Tue, May 19, 2015 at 5:59 PM Duy Tran Phuoc tranpdu...@gmail.com wrote:
Hi everyone,
I try to compile GROMACS 5.0.5 on Fujitsu PRIMEHPC FX-10 with the
Hi,
No, but you can probably use -mcn to get an index group of the atoms, and
work backwards from there. See gmx clustsize -h
Mark
On Tue, May 19, 2015 at 6:07 PM pratibha kapoor kapoorpratib...@gmail.com
wrote:
Hi,
I have used g_clustsize to count the number of molecules (they differ by
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