Hi,
Please do not cross-post your mailing list questions to individuals unless they
have solicited your inquiries. I know nothing about QMMM/MOPAC :-)
The best I can suggest is that you haven't made the MOPAC libs available in the
default linking path. Please consult whatever installation docum
So, what should I aim for when running an NPT simulation?
Pooja
On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren wrote:
> Is that really that surprising?
>
>
>
> You have variations of the order of 100s of bar and are looking for an
> average that is 1.0
>
>
>
> What you are observing is nothing o
Justin,
> Have you tried using the sd integrator? That's what the authors of this paper
> used. I don't know if there are stability issues with md vs. sd, but it's a
> starting point.
That does appear to be the issue. We have repeated the pentane in octanol
lambda runs and it completed withou
Is that really that surprising?
You have variations of the order of 100s of bar and are looking for an
average that is 1.0
What you are observing is nothing out of the ordinary, from my
experience and what others have discussed here on the emailing list.
Catch ya,
Dr. Dallas Warren
M
Hi
Yes, the fluctuations are large but even the average pressure hasn't
converged. Its close 2.5 bar. RMSD ~600 bar.
Pooja
On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren wrote:
> See http://www.gromacs.org/Documentation/Terminology/Pressure for further
> details
>
>
>
> Catch ya,
>
> Dr. Dallas
See http://www.gromacs.org/Documentation/Terminology/Pressure for
further details
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
Dear sir,
thanks in advance
When i type the following command in gromacs directory
./configure --with-qmmm-mopac --disable-float
it configure successfully
but when i compile by make command i got the following error at the end of my
compilation
libs/libgmxpreprocess_d.a ../mdlib/.libs/libmd_d
What pressure has it reached?
Probably best graph the pressure versus time plot for the run and show
that.
I suspect what you are concerned about is the fact that with pressure
coupling, the pressure can fluctuation from step to step, very widely,
100s atm is not out of the question.
Catc
Hi,
I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.
The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.
I don;t understan
Thanks Mark :).
On Tue, Sep 7, 2010 at 10:06 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Sunday, September 5, 2010 8:19
> Subject: [gmx-users] Tables and forcefield parameters
> To: Discussion list for GROMACS users
>
> > Hi,
> >
> > ques1:
> > I have 3
Dear Gmxers,
I am working on a new project and I plan to do some molecular dynamic
simulation on an engineered GFP molecule. I have been searching for the
parameters for the GFP chromophore without success. Could some one help me? Any
reference or parameters will be appreciated.
Thanks,
Juju
- Original Message -
From: Sai Pooja
Date: Sunday, September 5, 2010 8:19
Subject: [gmx-users] Tables and forcefield parameters
To: Discussion list for GROMACS users
> Hi,
>
> ques1:
> I have 3 energy groups.
> I am interested in using tables for LJ and coulomb interactions for
> Gr
- Original Message -
From: Sebastian Breuers
Date: Tuesday, September 7, 2010 17:47
Subject: Re: [gmx-users] g_covar & g_anaeig problems
To: gmx-users@gromacs.org
> Hey,
>
> taking fewer atoms by ignoring the hydrogens is a good advice.
> Thanks a lot.
That's just the tip of the iceb
- Original Message -
From: nahren manuel
Date: Tuesday, September 7, 2010 20:33
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: Discussion list for GROMACS users
---
| > Dear Gromacs Users,
>
> Tsjerk,
>
> the original
- Original Message -
From: David de Sancho
Date: Wednesday, September 8, 2010 8:04
Subject: [gmx-users] Re: Restarts: Truncation of file *.xtc failed
To: gmx-users@gromacs.org
> Hi
> Thanks Greg for your answer.
> Yes, my simulation is in fact pretty long and its files are considerably
- Original Message -
From: Yongchul Chung
Date: Wednesday, September 8, 2010 4:10
Subject: Re: [gmx-users] Restarts: Truncation of file *.xtc failed
To: Discussion list for GROMACS users
> Hi,
>
> How big is your file? I assume since you are running 18ps simulation, it
> might be
> > 1- Actually since I was focusing on rdf for C-C I didnt explain my
> > understanding from that post well. Anyway, I have only C and H in
the
> > system and no protein. You mean I have to make separate groups of C
> and
> > H for all polymer chains by hand? I trying to find a more smart way
> of
Hi
Thanks Greg for your answer.
Yes, my simulation is in fact pretty long and its files are considerably
large. The size of the xtc files is approximately ~2 GB when I am trying to
do the restart.
I thought on the contrary that my problem was related to another post in
today's list (
http://lists.g
Moeed wrote:
Dear experts,
I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom
type CU+2. I am not using such atom type at all! Could you please help
me what wrong is. Thanks.
No one can tell unle
Dear experts,
I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.
grompp -f *.mdp -c *.gro -p *.top -o out >
Vishal Agarwal wrote:
Dear Gromacs Users,
Is there a way to convert the hessian.mtx file into a readable format
using any of the gromacs utilities?
gmxdump -mtx
g_nmeig
-Justin
Any help on this would be highly apprecaited..
Thanks,
Vishal
--
Dear Gromacs Users,
Is there a way to convert the hessian.mtx file into a readable format using
any of the gromacs utilities?
Any help on this would be highly apprecaited..
Thanks,
Vishal
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
Hey Nahren,
>
> sed -i '/^ATOM.*O2/d' DIMER.pdb
>
> Am i going wrong here?
You should try :) But it looks quite okay to me ;)
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
Un
Hi,
How big is your file? I assume since you are running 18ps simulation, it
might be big. I remember there's a problem with gromacs not being able to
truncate file size >4Gb.
Greg
On Tue, Sep 7, 2010 at 8:04 AM, David de Sancho wrote:
> Dear Gromacs users
> I am experiencing a problem with
Hi there,
I am trying:
~/Downloads/gromacs-4.5.1/build% cmake -DGMX_OPENMM=ON ..
~/Downloads/gromacs-4.5.1/build% make mdrun
[ 1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[ 1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/
Moeed wrote:
Hello Justin,
1- Actually since I was focusing on rdf for C-C I didnt explain my
understanding from that post well. Anyway, I have only C and H in the
system and no protein. You mean I have to make separate groups of C and
H for all polymer chains by hand? I trying to find a m
Hello Justin,
1- Actually since I was focusing on rdf for C-C I didnt explain my
understanding from that post well. Anyway, I have only C and H in the system
and no protein. You mean I have to make separate groups of C and H for all
polymer chains by hand? I trying to find a more smart way of doin
Hi,
For the moment you can add the option -nt 1 to mdrun, which will make it run
without problems.
Berk
From: per.lars...@sbc.su.se
Subject: Re: [gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode
analysis
Date: Tue, 7 Sep 2010 16:12:28 +0200
To: gmx-users@gromacs.org
This h
This has been fixed with Berk's commit c06ee471...
The error was not related to GB, but rather a combination of domain
decomp.+nm+cut-offs.
Cheers
/Per
6 sep 2010 kl. 11.38 skrev Ehud Schreiber:
> Dear GROMACS users,
>
> I am encountering a couple of issues when trying to perform normal mode
Maria, try this. There actually is a lot of this on the mailing list,
so I suggest checking it a little deeper for your next querry, or at
least outlining how you looked and what you found so that it is clear
you have tried.
Also, read about pull_pbcatomN and think carefully about how you w
If using links or simply copying in /usr/local/bin I don't mind, but it
would easier, at least for me, once installing gromacs from source to be
able to have the gmx bins in /usr/local/bin and, of course, be able to
uninstall all gromacs as well (and undoing links or removing copies from
/usr/local
The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.
[ position_restraints ]
; ai functfc
...
3 1 1000 0 0
How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially
On 9/7/10 1:19 PM, Alan wrote:
I am trying release-4-5-patches and now I can see it's compiling and
installing. However, 'make install' puts the bins only in
/usr/local/gromacs/bin and I don't have (or don't find) how to 'make
links' or similar to have the gmx bins in /usr/local/bin.
I am us
Dear Gromacs users
I am experiencing a problem with restarts in a REMD simulation with explicit
solvent in Gromacs 4.0.5. I am trying to continue a set of simulations that
finished after the maximum time in our cluster queue had been reached.
Therefore I just directly (i.e. without modifying my inp
Thanks Carsten.
I am trying release-4-5-patches and now I can see it's compiling and
installing. However, 'make install' puts the bins only in
/usr/local/gromacs/bin and I don't have (or don't find) how to 'make links'
or similar to have the gmx bins in /usr/local/bin.
I am using cmake.
Thanks,
Hi Alan,
'bleeding edge' gromacs development is as always in the 'master' branch.
The latest bugfixes for the 4.5.x versions you are going to find in the
'release-4-5-patches' branch.
Carsten
On Sep 7, 2010, at 12:09 PM, Alan wrote:
> Hi there,
>
> Now that gromacs 4.5.1 is released I was won
Poojari, Chetan wrote:
Hi,
I have done MD simulations of membrane-protein. I want to calculate
interaction energies between protein and headgroup, protein and hydrophobic
core (in the bilayer). Please can anyone suggest me the method that should be
followed to carry out these analysis.
Plea
maria goranovic wrote:
I want to restrain certain atoms of my simulation to the plane
perpendicular to the bilayer normal, and at the bilayer center. Can
someone please provide a quick guide on how to do this? I read the
pull-code options, but restraining to a plane did not seem possible?
shiva birgani wrote:
Dear Justin
I want to simulate a protein in the high temperature (338 K).
I wan to know changing of ref_t in mdp file is enough and there is not
any other parameter to be changed in this regard?
If you need to generate velocities, then gen_temp should also be set to this
Hi,
I have done MD simulations of membrane-protein. I want to calculate interaction
energies between protein and headgroup, protein and hydrophobic core (in the
bilayer).
Please can anyone suggest me the method that should be followed to carry out
these analysis.
kind regards and best wishes,
Dear Gromacs Users,
Tsjerk,
the original file did not contain OXT, as you can see, it has O1 &
O2, so I removed the O2 from the PDB and renamed O1 to OXT.
ATOM 2841 HG CYS R 283 -24.270 89.566 -4.957 1.00 0.00 H
ATOM 2842 C CYS R 283 -25.867 92.922 -7.562 1.00
Hi Nahren,
Can you paste your actual command line where you used sed?
Cheers,
Tsjerk
On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel wrote:
> Dear Gromacs Users,
>
> thanks for all your suggestions.
>
> Tsjerk, I did try your idea, but unfortunately doesn't seem to work.
>
> the pdb file is sh
Dear Gromacs Users,
thanks for all your suggestions.
Tsjerk, I did try your idea, but unfortunately doesn't seem to work.
the pdb file is shared here :
http://www.4shared.com/account/file/ijofD83b/DIMER.html
newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh
Fatal error:
Atom OXT in residu
Hi there,
Now that gromacs 4.5.1 is released I was wondering which branch should I
checkout if I want to test the bleeding edge gromacs development.
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Roa
I want to restrain certain atoms of my simulation to the plane perpendicular
to the bilayer normal, and at the bilayer center. Can someone please provide
a quick guide on how to do this? I read the pull-code options, but
restraining to a plane did not seem possible?
--
Maria G.
Technical Univer
Hi,
> One work-around for the -chainsep situation you've observed is to remove or
> rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when
> it tries to merge the chains. It should be taking care of that itself, but
> handling it yourself might help. pdb2gmx can probably
Hi,
I had sent a wrong PDB file, right one sent offlist.
Cheers
Silvio
Il Tuesday 07 September 2010 10:06:15 Per Larsson ha scritto:
> Hi!
>
> I am currently working on another issue with the GB-double precision loops.
> I'll include this as well.
> But your pdb-file only contains 1 residue w
Hi!
I am currently working on another issue with the GB-double precision loops.
I'll include this as well.
But your pdb-file only contains 1 residue with the name UNK (by openBabel).
Could you please send me another pdb-file that reproduces this error off-list,
and I'll get to it.
Cheers
/Per
Dear friends,
when trying to run a double precision vanilla MD, version 4.5.1, with a small
hairpin molecule (248 atoms) in implicit solvent (generalized Born
approximation) this is what I get:
-
Getting
Hey,
taking fewer atoms by ignoring the hydrogens is a good advice. Thanks a
lot.
I was wondering if a more appropriate error message could be generated
before the program messes around in the memory. The program acts as if
it could handle the system size and then crashes with a Segmentation
Dear Justin
I want to simulate a protein in the high temperature (338 K).
I wan to know changing of ref_t in mdp file is enough and there is not any
other parameter to be changed in this regard?
and how much the results of this type of simulation (in high temperature) is
reliable?
thanks in advance
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