OK, but with Berendsen you're also not observing physics. Your call.
Mark
On Wed, May 14, 2014 at 3:50 AM, Steven Neumann s.neuman...@gmail.comwrote:
Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no
crashes observed.
On Tue, May 13, 2014 at 2:08 PM, Mark Abraham
Rather, find out what non-bonded scheme your models were parametrized to
use, and use that! These are often not free parameters!
Mark
On May 15, 2014 6:47 AM, sujithkakkat . sujithk...@gmail.com wrote:
Hello Justin,
I looked at the energy components. What I find is that Short Range LJ is
First, check your install of MPI works on a simple test program. Then,
check that GROMACS cmake picked up the MPI you expected, and that that's
really the one you're using at run time.
Mark
On Thu, May 15, 2014 at 3:28 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I try to submit Gromacs
On Thu, May 15, 2014 at 8:04 AM, ravikumarvenkatraman
ravikumarvenkatra...@gmail.com wrote:
Dear Gromacs user's,
Could anybody tell me how to
calculate energy autocorrelation function using Gromacs. I need it to take
statistically uncorrelated snapshots
05:35 PM, Mark Abraham wrote:
First, check your install of MPI works on a simple test program. Then,
check that GROMACS cmake picked up the MPI you expected, and that that's
really the one you're using at run time.
Mark
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Gromacs Users mailing list
* Please search the archive at http
On May 16, 2014 7:03 PM, Juan Munoz-Garcia
juan.munoz-gar...@bioch.ox.ac.uk wrote:
Dear Justin,
thank you. I’ve tried the following but neither of them worked, I get the
same result.
trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol
-ur compact
trjconv -f input.gro
Unstable models or unstable initial conditions will behave unpredictably.
Unfortunately you've not given us much to go on.
Mark
On May 16, 2014 6:08 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
On 5/16/14, 11:37 AM, Nilesh Dhumal wrote:
Hello,
I am running the simulation for ionic
What Michael said, and if your .mdp setup triggers a code path for which
the implementation changed between 4.0.7 and 4.5.5 (like it did for at
least twin-range), then you should see different behaviour. But I guess
we'll have to keep making unproductive guesses.
Mark
On Fri, May 16, 2014 at
Your simulation seems too small to parallelize in the way you/mdrun tried.
But we need more information to be sure.
Mark
On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud...@gmail.com wrote:
Hi Everyone
I need some help. With my mdrun command I am getting this following error
.
On May 16, 2014 11:36 PM, Koki Yokoi kyo...@uwm.edu wrote:
Hello. I am currently using GROMACS4.6.5 and trying to simulate a
fluorescent protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine
receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme
part(res#1002-1161), so I removed
file??
Thanks
Lovika
On Sat, May 17, 2014 at 11:35 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Your simulation seems too small to parallelize in the way you/mdrun
tried.
But we need more information to be sure.
Mark
On May 17, 2014 7:33 AM, Lovika Moudgil lovikamoud
First, you need a membrane for simulating this protein at all
realistically. Second, you need to consider what residue protonation states
are relevant for the system you are trying to model - neither the contents
of the PDB file nor the defaults of the topology building program can be
used
You seem to be following
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
which is good. But it's hard to help when we don't know what you think
doesn't work means. Make sure that the things you think are whole in
md_0_1.tpr actually are. Visualize your intermediate
from
wonder.
Albert Einstein
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark
Abraham [mark.j.abra...@gmail.com]
Sent: Monday, May 19, 2014 4:31 PM
To: Discussion list
Probably garbage in, garbage out. However you're measuring the density
probably depends on share/top/atommass.dat, which relies on matching atom
names to infer atom types and thus masses. If your atom names don't follow
its assumptions... at least some tools warn about this in the output. Did
the
...@gmail.comwrote:
Thank you Mark,
My Bad. Now fixed.
Hope the simulations I did before were not affected, I had defined
atomtypes with the correct mass in the .itp file used.
Sujith
On Wed, May 21, 2014 at 12:59 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Probably garbage in, garbage
On Wed, May 21, 2014 at 12:00 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/21/14, 5:22 AM, Nicola Staffolani wrote:
Dear GROMACS user community,
I have the following problem: I would like to let a simulation run on a
computer where another simulation, prepared by another user, is already
On Thu, May 22, 2014 at 5:31 PM, Thomas C. O'Connor tocon...@jhu.eduwrote:
Hey,
Yes, everything runs fine if I work on one node with one or more GPU's. The
crash occurs, similar to the previous mailing list post:
http://comments.gmane.org/gmane.science.biology.gromacs.user/63911
It
Hi,
The usual workflow to fix these kinds of pbc issues can be found here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
On Thu, May 22, 2014 at 9:48 PM, Steve Seibold steve...@ymail.com wrote:
I ran a 8 ns simulation on a small protein in a water box
First, find something out. Does the installation work for any other
simulation? What does the log file say? Have you equilibrated your system
first? Does another integrator or thermostat work?
Mark
On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote:
Hello gmx-users,
I tried to
of gen_temp.
Thank you,
Yu
2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com:
First, find something out. Does the installation work for any other
simulation? What does the log file say? Have you equilibrated your system
first? Does another integrator or thermostat work?
Mark
.mdp files of whatever it is you're
doing.
Trying to provide help based on fragmented information is very
hard,
and
it could be a simple matter of some incorrect settings, but we can't
tell.
-Justin
2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com
Hi,
Decoupling both q and vdw at the same time is not a good idea. You should
observe that at nearly-disappeared lambda, the error bars grow dramatically.
Mark
On Tue, May 27, 2014 at 5:38 PM, Fahimeh
fahimeh.baftiza...@googlemail.comwrote:
Hi everyone,
I am computing solvation free energy
.
That will help establish where the problem lies.
Mark
I really appreciate your help
Fahimeh
On Tue, May 27, 2014 at 12:20 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Decoupling both q and vdw at the same time is not a good idea. You should
observe that at nearly-disappeared lambda
There should be. See
g_select -select 'help arithmetic'
Mark
On Wed, May 28, 2014 at 3:38 PM, mojdeh akhavan mojdeh.akha...@gmail.comwrote:
Dear gmx users,
Hi
I have a quation about g_select. Is it posssible to use mathematical
expressions in g_select?
For example, I want to select
Hi,
The source of the issue with #1222 was never established, so we can't know
if your situation is related. What were your mdrun command lines and .mdp
settings?
Mark
On Wed, May 28, 2014 at 6:33 PM, albert ardevol albert.arde...@gmail.comwrote:
-- Forwarded message --
Hi,
I do not think there is any ability in GROMACS to mix LJ and Buckingham.
Each particle can have only one set of non-bonded parameters, so there is
no sensible way to express the interaction between the sets of atoms
natively using each type of interaction.
Mark
On May 29, 2014 2:28 AM,
Hi,
That seems like a bug. What GROMACS command and version produced it?
Mark
On May 29, 2014 6:40 AM, bharat gupta bharat.85.m...@gmail.com wrote:
Thanks you all for your responses. As far the chain name is concerned, that
can be worked out by a simple script. But I found another issue in
.
But still, whats the solution to my problem. I will post this query in
Pymol mailing list also.
On Thu, May 29, 2014 at 2:56 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
That seems like a bug. What GROMACS command and version produced it?
Mark
On May 29, 2014 6:40 AM
There's no support in genion for that.
Is there data to show that the concentration profile of ions varies with
potential at the relevant concentration and distance scales?
Mark
On Thu, May 29, 2014 at 9:04 AM, Atila Petrosian atila.petros...@gmail.com
wrote:
Dear all
I do not like to
On Thu, May 29, 2014 at 11:24 AM, #ZHANG HAIPING# hzhang...@e.ntu.edu.sg
wrote:
Dear gromacs user:
Can any tell me how to determine the cut-off parameter e.g. rcoulomb,
rvdw in the mdp file.
This should generally be determined in consultation with the literature on
using the forcefield you
Hi,
Yes. There was once something like this, but it didn't work and has been
removed.
Mark
On Thu, May 29, 2014 at 9:57 AM, Atila Petrosian atila.petros...@gmail.com
wrote:
Dear Mark
Thanks for your reply.
Are you sure there's no support in genion for what is my interest?
--
Gromacs
On May 29, 2014 2:28 AM, Chetan Mahajan chetanv...@gmail.com wrote:
Dear All,
I just came across this fantastic capability of Gromacs, user-specified
potential functions, which can let me use LJ potential for some atom pairs
whereas Buckingham for some others. However, I have a doubt about
for buckingham). Thus, nbfunc=1 should work even if some pairs interact via
buckingham while others by LJ.
Please comment.
Thanks
Chetan
On Fri, May 30, 2014 at 12:02 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On May 29, 2014 2:28 AM, Chetan Mahajan chetanv...@gmail.com wrote
Yes, you can just compile this tool, but you still need to configure a new
GROMACS build to use libgsl before make g_kinetics can be useful.
Mark
On Sat, May 31, 2014 at 4:17 AM, bharat gupta bharat.85.m...@gmail.com
wrote:
Hi,
While issuing the command g_kinetics, I got an error saying
should be able to calculate cross term and apply table.xvg, without
the need to enter C an A for that pair explicitly as an additional term in
topology file. I need to confirm.
Thanks
Chetan
On Fri, May 30, 2014 at 2:38 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Yes. Three parameters
Hi,
Please check out the equations and non-bonded combination rules in chapter
4 of the manual, and the units in chapter 2.
Mark
On Sat, May 31, 2014 at 2:43 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear justin,
Could tell me how do I convert those non-bonded values between CHARMM and
gromos431
Hi,
What's the smallest relevant neutral system you can think of? Test your
implementation of your model on that, on a local machine, not a
supercomputer ;-) If there's any diagnosis of why the crash happens, it
will be in the log file. But you seem like you have far too many variables
to know
during MD.
However, that should not matter, since code is crashing very initial step
of MD run).
That could mean anything, including that your MPI compilation of GROMACS is
not working. Simplify!
Mark
Thanks
Chetan
On Sun, Jun 1, 2014 at 5:11 PM, Mark Abraham mark.j.abra...@gmail.com
On Tue, Jun 3, 2014 at 2:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/3/14, 6:51 AM, Bikramjit Sharma wrote:
Hi all,
I tried to generate topology file for benzene (as a trial) using
topolbuild1_3. The itp file generated is (ffben.itp in my case)
#define _FF_GAFF
#define _FF_AMBER
Hi,
What makes you think the PME algorithm, rather than your choices of
settings for it (and twenty other things), is the problem?
Mark
On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmoja...@gmail.com
wrote:
Dear All users,
I have encounter this error:
-
Fatal
On Wed, Jun 4, 2014 at 1:01 AM, gmail wenjin.brooks...@gmail.com wrote:
Dear gmx-users,
I have some questions on the way that gromacs remove the rotation around
the center of mass when set comm-mode = Angular”
I have checked the related code for removing the rotation and have a
question on
On Wed, Jun 4, 2014 at 12:42 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com
wrote:
Dear Mark,
Thank you for your reply.
When you do not change any parameters except one thing in mdp file(PME to
ewald as the paper said that)and then your system converges, for me it means
the problem is
Hi,
It's hard to understand what you're doing, but take care to distinguish
atom name, residue name, and moleculetype name, which can all be different
depending on the GROMACS version and force field.
Mark
On Wed, Jun 4, 2014 at 10:50 AM, elham tazikeh elham.tazi...@gmail.com
wrote:
Dear
On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote:
Dear gromacs community,
How does the gromacs calculate Intra molecular force correction (To correct
the unwanted intra molecular force in Fourier space especially for rigid
molecules)? I couldn't find that information listed
settings are not the only determining factors of the
validity
of the model physics) and evidence of what you're deciding is equilibrated,
stable, etc (i.e. real numbers and output from whatever relevant analysis).
-Justin
On Wed, Jun 4, 2014 at 4:35 PM, Mark Abraham mark.j.abra...@gmail.com
Choosing appropriate output-frequency settings, nsteps to cap your file
size, and mdrun -noappend is likely your best approach.
Mark
On Wed, Jun 4, 2014 at 8:54 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Tue, Jun 3, 2014 at 10:35 PM, Carlos Familia carlosfami...@gmail.com
wrote
On Jun 5, 2014 8:34 AM, #ZHANG HAIPING# hzhang...@e.ntu.edu.sg wrote:
Dear gromacs user：
I have used follow .mdp to run the replica exchange simulation, after the
simulation, I find the water box become much larger in high temporature
replicas, can anyone tell me how to solve this? By the way,
On Jun 5, 2014 8:24 PM, Ali Khan ak...@virginia.edu wrote:
Hi all,
I don't know if anyone has experienced this problem before, but I figure I
ask. I have several times run a simulation on a 135A x 135A POPC membrane
acquired fro the charmm-gui website. I wanted now to simulate one that was
-boun...@maillist.sys.kth.se 代表 Mark Abraham
mark.j.abra...@gmail.com
发送时间: 2014年6月5日 16:06
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] the water box become much larger in high temporature
replicas after replica exchange simulation
On Jun 5, 2014 8:34 AM, #ZHANG HAIPING# hzhang
exclusions are
dealt with by all these codes the same way. Note carefully the use of erf
vs erfc in the corrective terms.
Mark
Sumith YD
Date: Wed, 4 Jun 2014 21:26:31 +0200
From: Mark Abraham mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Cc: Discussion list
that equation
in the source code too.
Sumith YD.
Date: Thu, 5 Jun 2014 20:43:03 +0200
From: Mark Abraham mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] Intra molecular force correction for SPME
Message-ID
What did you learn from the performance output at the end of the log file?
Mark
On Thu, Jun 5, 2014 at 9:26 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I've got a GPU machine with two GTX780 Ti card. Here is my configurations:
Intel Xeon E5-2690V2, 10 Cores, 3.0 GHz
Silent Cooling
On 06/06/2014 02:08 PM, Mark Abraham wrote:
There's only one rank, so you can only be using one GPU!
Mark
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Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org
the hardware settings to make
sure, that SLI is still enabled in the hardware. Please contact us for
this, a technician can control all the hardware settings with you.
thank you very much.
Albert
On 06/07/2014 02:20 AM, Mark Abraham wrote:
The Nodes column has the vakue one. It is a poor name
Hi,
One simple solution is to subscribe with a different email address.
Mark
On Thu, Jun 12, 2014 at 9:54 AM, X Rules xru...@live.com wrote:
This is the 4th time I am thrown out of the list by some random phishing
email and I am done with this. If I am thrown out this time (I know I will
On Thu, Jun 12, 2014 at 4:11 AM, 陈功 gchen...@gmail.com wrote:
Dear gromacs users,
I have doubts that whether I should use two groups to control the
temperature or just one since there are just 604 hundred Protein beads and
6+ solvent beads. It is said that two groups are more
Hi,
I've no idea if mailman even has that option, or the KTH IT admins would be
willing to set it up, but that's not worth exploring until automatic
unsubscription is known to be a problem for more than one email address.
Mark
On Thu, Jun 12, 2014 at 1:34 PM, X Rules xru...@live.com wrote:
Hi,
Please see tables in chapter 5 of the manual.
Mark
On Sat, Jun 14, 2014 at 8:50 AM, akari karin j.akarika...@gmail.com wrote:
dear gromacs users,
i am simulating carbon nanotubes. i am having some problems with my
interaction potential in the forcefield.itp file.
my forcefield.itp
On Sat, Jun 14, 2014 at 2:06 AM, Rini Gupta rinisgu...@gmail.com wrote:
Dear gmx-users,
Sorry, for asking such a simple question. But I didn't get any
satisfactory answer searching through mailing lists.
I have prepared a mixed bilayer system containing 300 lipids with box
size 10 10 14
Hi,
It means your simulation is
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
On Tue, Jun 17, 2014 at 11:39 AM, h.aliza...@znu.ac.ir wrote:
Dear all,
In one of my simulations when I use the command
mdrun -v -deffnm nvt
I face with this fatal error:
Too many LINCS
Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2
and HB3 and use sed (or your text editor) to do the replacement.
Mark
On Tue, Jun 17, 2014 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/17/14, 1:51 PM, Matthew Stancea wrote:
Dr. Justin Lemkul,
Ah I
ie. do the replacement on your input coordinate file, not the .rtp!
On Tue, Jun 17, 2014 at 10:35 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2
and HB3 and use sed (or your text editor) to do the replacement.
Mark
, but it is odd. Due to periodicity we
have,
output of any calculations will remain the same. Again, with -all
option
for refcoord scaling, this movement of water and slab DOES NOT occur.
Thanks a lot!
regards
Chetan
On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham
mark.j.abra...@gmail.com
Indeed, it does some similar things, but the scope of the respective
optimizations is different.
Mark
On Jun 18, 2014 5:39 PM, Soren Wacker swac...@ucalgary.ca wrote:
Then I misunderstood the function of -tunepme.
I thought it replaces g_tune_pme, but that is apparently not the case.
Thanks
Hi,
It sounds like your practical options are to build some larger fragments to
use when required, or generate your topology with something else, e.g. a
custom script. pdb2gmx was built with slightly-branched polymers in mind,
not much else.
Mark
On Thu, Jun 19, 2014 at 6:11 PM, Soren Wacker
Hi,
It would be miraculous if there was a good solution for all observables. A
rigid, symmetric 3-point water molecule without VDW parameters on the the
hydrogen atoms has 2 spatial, 2 charge, and 2 VDW parameters. That's not
much freedom, and most of the 6-parameter space is obviously wrong,
Yes. Please start by reading the reply Justin made a few days ago. Your
normal is unknown to us.
Mark
On Jun 24, 2014 10:29 PM, Tom dna...@gmail.com wrote:
Dear Gromacs Developers and Experts:
I noticed that the performance of gromacs on Cray linux clusters is only
36.7% of the normal.
Indeed. REST implemented in PLUMED seems a good bet.
Mark
On Jun 24, 2014 11:50 PM, HANNIBAL LECTER hanniballecte...@gmail.com
wrote:
I would think of using Replica Exchange with Solute Tempering in this case.
Look at the paper as to how one can implement this in Gromacs (doi:
If you're happy that such parameters might work with your intended force
field, then you only need to build them into a topology. Assuming you have
some GROMACS experience, check out the relevant parts of chapters 4 and 5
of the manual.
Mark
On Jun 25, 2014 4:01 AM, 라지브간디 ra...@kaist.ac.kr wrote:
On Jun 25, 2014 8:15 AM, suhani nagpal suhani.nag...@gmail.com wrote:
Greetings
I have been trying to run a few set of simulations using high number of
processors.
Using the tutorial -
http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf
I have done
On Wed, Jun 25, 2014 at 5:53 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Jun 25, 2014 8:15 AM, suhani nagpal suhani.nag...@gmail.com
wrote:
Greetings
I have been trying to run a few set of simulations using high number of
processors.
Using the tutorial
On Fri, Jun 27, 2014 at 5:27 AM, Suman Chakrabarty
chakrabarty.su...@gmail.com wrote:
Hello!
1. It seems I have encountered a minor bug (?) in repl_ex.c for
version 4.6.x (for NPT simulations only):
Line 880 (in version 4.6.5):
fprintf(fplog, dpV = %10.3e d = %10.3e\nb,
That thread referred to the Cray compilers (these machines ship several),
but whether that is relevant we don't know. Showing the top and bottom .log
file chunks is absolutely critical if you want performance feedback.
Mark
On Jun 26, 2014 10:55 PM, Tom dna...@gmail.com wrote:
Justin,
I
://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0
http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz
Happy simulating!
Mark Abraham
GROMACS development manager
--
Gromacs Users mailing list
is now feature-stable.
Is this a typo because I thought the official release is production
quality.
Indeed, they are. I have fixed my copy-paste error, now. Sorry about that!
Mark
Best Wishes,
Ali Khan
On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi
version: 1.55.0 (internal)
On 29 June 2014 21:53, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi GROMACS users,
The official release of GROMACS 5.0 is available!
What new things can you expect?
* GROMACS now uses a combination of *C++98* and C99, so you will need
On Thu, Jul 3, 2014 at 9:17 AM, Dawid das add...@googlemail.com wrote:
Hi,
I have a following issue. Genbox seems to add a water molecule inside small
protein cavity and it does not belong there. Can I manually remove it from
*gro file?
Yes, but you need to make a matching change to the
http://www.gromacs.org/Documentation/Errors
On Thu, Jul 3, 2014 at 6:24 AM, dhaval patel pateldhaval...@gmail.com
wrote:
*Fatal error:*
25 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This
-07-03 9:55 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com:
On Thu, Jul 3, 2014 at 9:17 AM, Dawid das add...@googlemail.com wrote:
Hi,
I have a following issue. Genbox seems to add a water molecule inside
small
protein cavity and it does not belong there. Can I manually remove
Magnus LundborgPieter
Meulenhoff
*
*Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
*
*Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers
*
*Peter Tieleman Christian Wennberg Maarten Wolf *
*and the project leaders:*
*Mark Abraham
Hi,
GROMACS doesn't make NFS go down, but it might expose the problem that
exists anyway - which happens frequently on clusters that aren't set up
appropriately. The GROMACS checkpoint process requires that the file system
be present, so that the checkpoint process can compute and record hash
On Fri, Jul 4, 2014 at 6:44 AM, wliu w...@itcs.ecnu.edu.cn wrote:
Hi,
I have a following issue:
I use the force field CHARMM22-CMAP (that is charmm27-CMAP) in gromacs
to calculate the chignolin.pdb, I want to know the energy items of just
this one conformation. I choose to run a very
PLEASE READ AND CITE THE FOLLOWING REFERENCE
--
Best regards,
Thom
Message: 1
Date: Fri, 27 Jun 2014 23:49:53 +0200
From: Mark Abraham mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users
Hi,
Seems like a straightforward task for the scripting language of your choice
- even grep and sed can do a decent job. Get rid of all but two of the DMA
atoms, change them to whatever ions suit you, and make matching changes to
your [molecules] section manually. You may need to reorder to have
://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.6
http://www.gromacs.org/Documentation/Installation_Instructions_4.6
http://gerrit.gromacs.org/download/regressiontests-4.6.6.tar.gz
Happy simulating!
Mark Abraham
GROMACS development manager
--
Gromacs Users mailing list
On Jul 9, 2014 7:39 PM, Ondrej Kroutil okrou...@gmail.com wrote:
Hi gromacs users and developers,
I have troubles with simulations of the system with surface (slab
geometry)
using GPU and Verlet cut-off scheme.
When I run this simulation on CPU everything goes right and ions dissolved
in the
That means mdrun exited abnormally, e.g. from some undiscovered bug, or
(more likely) from someone e.g. pressing Ctrl-C on their terminal, or such.
Mark
On Thu, Jul 10, 2014 at 5:46 AM, Andy Chao ac...@energiaq.com wrote:
Dear GROMACS Users:
I used the grompp command to run energy
On Fri, Jul 11, 2014 at 12:18 PM, Nidhi Katyal nidhikatyal1...@gmail.com
wrote:
Hello all
I am trying to run my job on 2 nodes by utilizing all available cores. On
each node of the cluster, we have two GPUs and two sockets with 8 cores
each.
Every time I am submitting the job, we find that
Hi,
I haven't really followed the thread, but one of
https://gerrit.gromacs.org/#/c/3686/ or https://gerrit.gromacs.org/#/c/3656/
might be a guilty party - e.g. see what happens if you check out their
respective parents.
Mark
On Fri, Jul 11, 2014 at 11:14 PM, Justin Lemkul jalem...@vt.edu
Hi,
I would not have thought that was possible, but the recommended solution is
to compile mdrun for the machine you plan to use it on. See
http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects
for some details.
Mark
On Tue, Jul 15, 2014 at 5:00 AM, Andy
Hi,
That's highly unusual, and suggests you are doing something highly unusual,
like trying to run on huge numbers of threads, or very large numbers of
bonded interactions. How are you setting up to call mdrun, and what is in
your tpr?
Mark
On Jul 17, 2014 10:13 PM, Yunlong Liu yliu...@jhmi.edu
... and stop using 5.0-rc1!
Mark
On Tue, Jul 22, 2014 at 1:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/21/14, 1:30 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
Hi Dear Gromacs Users,
I have been dealing with a problem, i run an MD of my sistem , and i see
problems with my energies due
Hi,
All sounds very weird. I would be suspicious of the fact that you haven't
set rvdw. I have no idea what rvdw-switch might do in this context, but I
definitely think you should verify that systems with just two particles
have the interaction strength you can compute manually.
Mark
On Mon,
On Mon, Jul 21, 2014 at 3:48 PM, Siva Dasetty sdas...@g.clemson.edu wrote:
Dear All,
I am running simulations of BMP2 protein and graphite sheet using implicit
solvent model (mdp file is pasted below). The graphite atoms are frozen in
the simulation and BMP2 is free to translate.
I got an
On Mon, Jul 21, 2014 at 1:20 PM, rss r...@leobian.com wrote:
Dear all,
I want to get a “multiple dihedrals” topology file, but encounter a
problem. The following are the details.
I got the dihedrals parameters of azobenzene (expressed
in Ryckaert-Bellemans form) from
Hi,
Sorry, that's a bug in the build system. You can comment out that error
message in CMakeLists.txt and everything will work fine. atan2f4 is
required only when building the BG/Q SIMD kernels, which cannot take place
on BG/P.
Mark
On Tue, Jul 8, 2014 at 9:49 PM, Xingcheng Lin
There's a nice table in chapter 5 of the manual that cross-references the
sections in chapter 4.
Mark
On Fri, Jul 18, 2014 at 11:40 AM, Yip Yew Mun yipy0...@gmail.com wrote:
Hi, I know certain functional forms are represented by certain integers in
the .itp files. As I’m constructing my own
Hi,
Please leave the discussion on the list. Others may wish to contribute or
learn from it! :-)
-- Forwarded message --
From: Yip Yew Mun yipy0...@gmail.com
Date: Thu, Jul 24, 2014 at 5:16 AM
Subject: Re: [gmx-users] Obtaining Positive Energy Values for Both
Potential and Total
running these CG
simulations.
Thanks again,
Brian
On Wed, Jul 23, 2014 at 4:09 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
All sounds very weird. I would be suspicious of the fact that you haven't
set rvdw. I have no idea what rvdw-switch might do in this context, but I
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