Hi,
Something went wrong earlier in your workflow. Check your log files, etc.
Mark
On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote:
Hi:
When I am running the ibi procedure, I get the following error message:
A coordinate in file
For just modifying a file, just doing make is sufficient. I would
recommend not installing the modified version (since you can run the
build/src/kernel/mdrun directly), or if you must install, to use the
suffixing options available in the ccmake advanced mode.
Mark
On Nov 13, 2013 2:48 PM, Jheng
Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely
Mark
On Nov 13, 2013 12:03 PM, hasthi durgs7kr...@gmail.com wrote:
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein
Hi GROMACS users,
GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
some noteworthy simulation performance enhancements (particularly with
GPUs!). We encourage all users to upgrade their installations from earlier
4.6-era releases.
You can find the code, manual, release
On Nov 10, 2013 10:04 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
Yes (unless you are using AMD cpus), per the installation instructions,
although you will probably do slightly better with GCC 4.7, and should not
do a new install of 4.6.2 after 4.6.3 is released. In particular, 4.6.2 has
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Szilard,
Thank you very much for your suggestions.
Actually, I was jumping to conclusions too early, as you mentioned AMD
cluster, I assumed you must have 12-16-core Opteron CPUs. If you
have an 8-core (desktop?)
Hi,
There's nothing GROMACS-specific here - something about your MPI
installation, configuration or use is pretty wrong, but we can't help work
out what.
Mark
On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar
chandrashe...@iisertvm.ac.in wrote:
Dear all
I encounter a problem while
On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling alex.bjorl...@gmail.comwrote:
Dear users,
I am investigating protein crystal packing artifacts by doing equilibrium
simulations starting from a crystal structure. I would like to know if the
relaxations i see are reproducible, in the sense that
Hi,
That shouldn't happen if your MPI library is working (have you tested it
with other programs?) and configured properly. It's possible this is a
known bug, so please let us know if you can reproduce it in the latest
releases.
Mark
On Fri, Nov 8, 2013 at 6:55 AM, Qin Qiao qiaoqi...@gmail.com
expect any improvement?
Run how and compared with what? Using an external MPI library within a
single node is a complete waste of time compared with the alternatives
(thread-MPI, OpenMP, or both).
Mark
On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
You will do
OK, thanks.
Please open a new issue at redmine.gromacs.org, describe your observations
as above, and upload a tarball of your input files.
Mark
On Fri, Nov 8, 2013 at 2:14 PM, Qin Qiao qiaoqi...@gmail.com wrote:
On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham mark.j.abra...@gmail.com
wrote
First, there is no value in ascribing problems to the hardware if the
simulation setup is not yet balanced, or not large enough to provide enough
atoms and long enough rlist to saturate the GPUs, etc. Look at the log
files and see what complaints mdrun makes about things like PME load
balance, and
I think either is correct for practical purposes.
Mark
On Thu, Nov 7, 2013 at 8:41 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Does it make more sense to use nose-hoover or v-rescale when running in
implicit solvent GBSA? I understand that this might be a matter of opinion.
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com wrote:
Dear Justin,
I am sorry for the late reply. I still can't figure it out.
It isn't rocket science - your two .mdp files describe totally different
model physics. To compare things, change as few things as necessary to
Hi,
It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
original paper's coulomb settings can be taken with a grain of salt for use
with PME - others' success in practice should be a guideline here. The good
news is that the default GROMACS PME settings are pretty good for
icc and CUDA is pretty painful. I'd suggest getting latest gcc.
Mark
On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote:
Hi,
I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22.
The configuration runs okay and I have made sure that I have set paths
Sounds like a non-GROMACS problem. I think you should explore configuring
OpenMPI correctly, and show you can run an MPI test program successfully.
Mark
On Thu, Nov 7, 2013 at 5:51 PM, niloofar niknam
niloofae_nik...@yahoo.comwrote:
Dear gromacs users
I have installed gromacs 4.6.1 with
...@gmail.comwrote:
Thank you, Mark. I think that running it on CPUs is a safer choice at
present.
On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
the
original paper's coulomb
If the long-range component of your electrostatics model is not
decomposable by group (which it isn't), then you can't use that with LIE.
See the hundreds of past threads on this topic :-)
Mark
On Thu, Nov 7, 2013 at 8:34 PM, Williams Ernesto Miranda Delgado
wmira...@fbio.uh.cu wrote:
Hello
-DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
make
make install
cd ..
rm -rf build
On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
icc and CUDA is pretty painful. I'd suggest getting latest gcc.
Mark
On Thu
I'd at least use RF! Use a cut-off consistent with the force field
parameterization. And hope the LIE correlates with reality!
Mark
On Nov 7, 2013 10:39 PM, Williams Ernesto Miranda Delgado
wmira...@fbio.uh.cu wrote:
Thank you Mark
What do you think about making a rerun on the trajectories
Count the number of O observed near each C singly and compare the four
numbers.
Mark
On Nov 6, 2013 4:57 PM, rankinb rank...@purdue.edu wrote:
Hi all,
I would like to calculate the number of water molecules around any of the
methyl carbon atoms of tert-butyl alcohol. Currently, I have
Hi,
They ought to, and we hope they do, but historically quality control of
analysis tools was threadbare, there is no testing of that kind of thing
now, and certainly no implied warranty. Especially at the existing price
point! ;-)
That comment could easily refer to (or be) an archaic code
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
Many thanks Justin. What is an appropriate cut-off value? My box size is
d=
0.5 nm; based on the definition of cut-off radius, its value shouble be
smaller than d/2; therefore
On Tue, Nov 5, 2013 at 12:55 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Richard,
1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test
gave me performance about 25ns/day for the explicit solved system consisted
of 68k atoms (charmm ff. 1.0 cutoofs)
gaves slightly worse
You need to configure your MPI environment to do so (so read its docs).
GROMACS can only do whatever that makes available.
Mark
On Tue, Nov 5, 2013 at 2:16 AM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi,
I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
32
Yes, that has been true for GROMACS for a few years. Low-latency
communication is essential if you want a whole MD step to happen in around
1ms wall time.
Mark
On Nov 5, 2013 11:24 PM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Szilard,
Thanks.
From Timo's benchmark,
1 node142
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi,
I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
fine till .configure command, but I am getting error at the make command :-
Error:
[root@cluster gromacs-4.5.7]#
The principle is the same as at
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
On Nov 3, 2013 6:55 PM, ali.nazari ali.nazari.a...@gmail.com wrote:
Dear Friends,
I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas
mixture, the same as mixture of O2 and N2, any
On Fri, Nov 1, 2013 at 4:04 AM, Xu Dong Huang xudonghm...@gmail.com wrote:
Dear all,
I would like to assess the probability distribution of particle bond
distance/length over the entire run, specifically I want to collect
possibly a histogram representation or even a regular plot. Would
They're http://en.wikipedia.org/wiki/C_preprocessor symbols that are
#defined elsewhere in the directory that contains that .rtp file. The
names/symbols probably map to the original force field literature. grep is
your friend.
Mark
On Fri, Nov 1, 2013 at 6:45 AM, charles
the queue and yes
I
will re-read PBS docs.
On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.com
wrote:
Mark,
The problem with one .tpr file set for 100ns is that when job number
(say
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Mark
Very thanks for your reply
To make this clear, center the trajectory on the water and watch the
time evolution in some visualization program.
I did your suggestion (center the trajectory on the
On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.comwrote:
I have need to collect 100ns but I can collect only ~1ns (1000steps) per
run. Since I dont have .trr files, I rely on .cpt files for restarts. For
example,
grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o
Hi,
Hard to know. LAM was discontinued over 4 years ago. You could have a flaky
file system. Unless you're trying to run a jobsover both machines over
network like Infiniband, you don't even want to use an external MPI library
- single-node performance with built-in thread-MPI will give much
but be unable to change its status to /hold/ because PBS does not
return its ID. Another problem is that if resources are available, job 5
could start before I ever get a chance to /hold/ it.
On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Mon, Oct 28, 2013 at 4
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey hariche...@yahoo.com wrote:
Dear Gromacs Users,
First, I would like to thank Dr. Lemkul for reply.
My problem description is as follows:
I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass
of all atoms from topology, it
)
Can anyone please help me to figure out what is going wrong here?
Many thanks
Anu
On Fri, Oct 18, 2013 at 6:21 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
OK. All GROMACS does
On Sat, Oct 26, 2013 at 2:07 PM, Santu Biswas santu.biswa...@gmail.comwrote:
Not working is too vague a symptom for anyone to guess what the problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com
wrote:
dear users,
I am
On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes tiagogome...@gmail.comwrote:
Hi,
I am relatively new to the gromacs environment and would like to optimize
performance for my mac pro (osx 10.6.8)
with 8 cores (16 in hyper-theading). I´ve read that one can use
the g_tune_pme, i guess with np =
On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear jkrieger
I used 2 times trjconv tool:
1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol
-center
Dear Mark
I selected
Not working is too vague a symptom for anyone to guess what the problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote:
dear users,
I am performing 500ps mdrun in vacuum for polypeptide(formed
by 10-residues leucine) using
Hi,
No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS threads to logical
cores, and warnings are written for various wrong-looking cases, but we
haven't taken the time to write a sane report of how GROMACS logical
threads
On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner ckut...@gwdg.de wrote:
On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS threads
Ja. No twin-range = no long-range :-)
Mark
On Thu, Oct 24, 2013 at 5:50 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
I think nstcalclr would only do something if you have longer range
interactions to calculate (lr means longer than rlist). Therefore
something has be longer than rlist for this to
As Justin said, there is no actual division between region 1 and 4.
Apparently you got the free diffusion you asked for! :-)
Mark
On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati
shahab.shari...@gmail.comwrote:
Dear Mark
Thank for your reply.
If I show my system as 4 regions, my system
On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote:
Hi,
We recently had a software upgrade in our cluster from gromacs 4.5.4. to
gromacs 4.6.3.. I need to continue an earlier simulation that had been run
in 4.5.4. using the .cpt, .tpr and .mdp.
Are there any issues with
On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am running a NPT simulation for cyclopropylchloride(1) in
50%water(100)+50%ethanol(100) using opls force field parameter .
After equilibration box size increases from 20 A to 70 A.
Really? Seems wildly unlikely
, if the model is parametrized reasonably.
So it should not phase-separate.
Vitaly
On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am running a NPT simulation
Hi,
Sounds very interesting. Can I have a test account, please?
The Lindahl group has some related work going on at
http://copernicus-computing.org/, automating large-scale simulation
workflows. I'm not sure yet whether we have any synergies! :-)
Cheers,
Mark
On Tue, Oct 22, 2013 at 4:34 PM,
Center on a particular lipid? Or head group?
Mark
On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
rectangular box.
I put drug molecule in 2 position: a) drug in the center of
Probably, make your broken molecules whole before passing them to grompp.
Mark
On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar sathishk...@gmail.comwrote:
The sum of the two largest charge group radii (13.336) is larger
than rlist(1.2) - rvdw/rcoulomb i am getting this error while running
Sounds like issues with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
strategies for coping found there.
Mark
On Mon, Oct 21, 2013 at 9:31 AM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Users,
I am doing protein-ligand MD simulations. I first
First, can you successfully add an ion that the force field already knows
about, like potassium? Second, does the force field know about chromium? If
not, who does?
Mark
On Sat, Oct 19, 2013 at 4:27 PM, Sathya bti027.2...@gmail.com wrote:
Hi,
I want to add chromium III ion into lipid
Can this file be opened in VMD itself?
Mark
On Oct 18, 2013 6:21 AM, anu chandra anu80...@gmail.com wrote:
Dear Gromacs users,
I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few
analysis. Unfortunately I ended-up with the following error.
successfully in VMD with the
file format option of ' AMBER coordinate with periodic box'. I am using VMD
1.9 version.
Regards
Anu
On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Can this file be opened in VMD itself?
Mark
On Oct 18, 2013 6:21 AM, anu chandra
You do need a C compiler, not a Fortran one, and IIRC gcc 4.6.2 has some
known issues. Please follow the instructions in the install guide and get
the latest compiler you can.
Mark
On Oct 17, 2013 8:30 AM, 张海平 21620101152...@stu.xmu.edu.cn wrote:
Dear professor:
When I install the Gromacs
Hi,
The log file gives a breakdown of how the minimum cell size was computed.
What does it say?
Mark
On Oct 17, 2013 5:17 AM, Christopher Neale chris.ne...@mail.utoronto.ca
wrote:
I have a system that also uses a set of distance restraints
The box size is:
7.12792 7.12792 10.25212
4.5 can only handle about 500-1000 atoms per processor. Details vary.
Mark
On Oct 17, 2013 5:39 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Thanks for you reply.
I am doing simulation for ionic liquids BMIM + CL. Total number of atoms
are 3328.
Nilesh
Assuming you're using LINCS,
(Redirected from gmx-developers)
The only way I can reproduce those symptoms is if I delete (or otherwise
make unreadable) various parts of src/gmxlib. You may have deleted some
files or been a different user at some point. I suggest you do a fresh
unpack of the tarball and try again.
Mark
On
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov suc...@gmail.com wrote:
Thank you, Mark!
It was already tried. I mean a fresh unpacking and further cmake run.
As for your first thought concerning a loss of access to some parts of
gmxlib:
[alemasov@nks-g6 gromacs-4.6.3]$ ls -l
, Mark Abraham mark.j.abra...@gmail.com wrote:
On Sat, Sep 21, 2013 at 2:45 PM, James jamesresearch...@gmail.com
wrote:
Dear Mark and the rest of the Gromacs team,
Thanks a lot for your response. I have been trying to isolate the
problem
and have also been in discussion with the support
http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and
http://www.gromacs.org/Documentation/Terminology/Pressure are useful here.
Mark
On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary
srinathchowd...@gmail.comwrote:
The barostat tries to equilibrate the system at the desired
Also, the precision was selected when the xtc file was written, ie in the
mdp file.
Mark
On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/14/13 7:56 PM, Leandro Bortot wrote:
Dear GROMACS users,
Does anyone know how significant is the difference between the
On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot
guillaume.chev...@gmail.com wrote:
2013/10/12 Mark Abraham mark.j.abra...@gmail.com
Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger
than
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue.
Google knows a lot more about it than anybody here ;-)
Mark
On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source
On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com
wrote:
Hi all,
I recently compared the total energy of 2 simulations:
lysozyme in water / NVE ensemble / single precision
lysozyme in water / NVE ensemble / double precision
... and what I found was quite ... disturbing
trust the results of single precision
simulations?
Regards,
Guillaume
*PS: I am not the only one encountering this behavior. In the literature,
this problem has already been mentioned:
http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1
2013/10/11 Mark Abraham mark.j.abra
Hi,
Since the release of 4.5.5, DSSP totally changed its command-line
interface. So old GROMACS code cannot work with new DSSP. You need to get
the old version of DSSP to use with old GROMACS, or new GROMACS code to
work with either DSSP.
Mark
On Thu, Oct 10, 2013 at 1:37 PM, Mass
Great! Many thanks Justin, and the CHARMM team!
Mark
On Tue, Oct 8, 2013 at 10:16 PM, Justin Lemkul jalem...@vt.edu wrote:
All,
I am pleased to announce the immediate availability of the latest CHARMM36
force field in GROMACS format. You can obtain the archive from our lab's
website at
I would generally not try to add it to an existing source repository.
Instead, follow one of the suggestions in
http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f
to
check out that version.
Mark
On Tue, Oct 1, 2013 at
the development
code from git. It is unwise to try to apply a patch from the master branch
on version 4.6; I doubt it would even work.
-Justin
Regards,
Tegar
On Tue, Oct 1, 2013 at 10:12 AM, Mark Abraham mark.j.abra...@gmail.com*
*wrote:
I would generally not try to add it to an existing
No, there's no way to do that. But you can monitor the output
trajectory file yourself, live.
Mark
On Thu, Sep 26, 2013 at 4:49 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Unlikely possible... But yeah, the feature might be handy.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 4:20 PM,
-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.6.3 (-:
Contributions from Mark Abraham, Emile Apol, Rossen
If diff says there are no changes, then you're not comparing with the file
you changed...
On Sep 25, 2013 1:59 PM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear Mark
The UNIX tool diff is your friend for comparing files.
Thanks for your suggestion. I used diff and sdiff toll
for
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a flexible molecule, e.g. define
= -DFLEXIBLE (or something). Check your water .itp file for how to do
it.
Mark
On Tue, Sep 24, 2013 at 10:25 PM, gigo g...@ibb.waw.pl wrote:
Dear GMXers,
Since
The FF+water combinations still work the same way they did 3 years
ago! :-) The important question is whether validation for the
observables has occurred. (And no relevant problems were seen). If the
paper does not support its decision to mix and match, go and ask them
why it was reasonable!
Mark
On Sep 23, 2013 9:23 AM, Jonathan Saboury jsab...@gmail.com wrote:
I tried minimizing a box of cyclohexanes and water. The first frame is
fine, but after that seemingly random lines form in vmd with the
cyclohexanes. The waters seem to minimizing just fine though.
I am sure I am just doing
On Sep 23, 2013 9:08 AM, marzieh dehghan dehghanmarz...@gmail.com wrote:
Hi every body
in order to protein- ligand docking, energy minimization was done by
GROMACS. I did the following steps for insulin pdb file:
1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
2- grompp -f
How do GAFF and acpype work?
Mark
On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote:
Dear prof,
can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand
and then use acpype to generate GAFF force field parameter for the NAD+ and
ligand?
--
On Mon, Sep 23, 2013 at 8:08 PM, Szilárd Páll szilard.p...@cbr.su.se wrote:
Hi,
Admittedly, both the documentation on these features and the
communication on the known issues with these aspects of GROMACS has
been lacking.
Here's a brief summary/explanation:
- GROMACS 4.5: implicit solvent
No, because then the state.cpt file would be redundant :-) All you can
do re-start from the beginning, because the .tpr file only has the
initial state. You can extend the number of steps, but you can't
magically produce the state after the first simulation just from the
initial one. (If you can,
You can try a run in implicit solvent to get a feel for the maximum
diameter of the protein while unfolding. You will not have any
certainty unless you can afford a box whose diameter is that of the
straight-line peptide...
Mark
On Sat, Sep 21, 2013 at 1:03 PM, aksharma arunsharma_...@yahoo.com
.
If there is a problem with GROMACS (which so far I doubt), we'd need a
stack trace that shows a line number (rather than addresses) in order
to start to locate it.
Mark
Gromacs version is 4.6.3.
Thank you very much for your time.
James
On 4 September 2013 16:05, Mark Abraham mark.j.abra...@gmail.com wrote
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury jsab...@gmail.com wrote:
I am doing this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
I have set up the randomly placed cyclohexane and water throughout the box.
The problem is when i try
On Thu, Sep 19, 2013 at 2:48 PM, Xu, Jianqing x...@medimmune.com wrote:
Dear all,
I am learning the parallelization issues from the instructions on Gromacs
website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But
I hope to get some advice about a correct way to run
The UNIX tool diff is your friend for comparing files.
On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati
shahab.shari...@gmail.com wrote:
Dear Tsjerk
Thanks for your reply
Before correcting the gro file, I knew that gro file is fixed format.
I did this correction very carefully.
Part of
Note that the group scheme does not reproduce the (AFAIK unpublished)
CHARMM switching scheme, either.
Mark
On Fri, Sep 20, 2013 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/19/13 9:55 PM, akk5r wrote:
Thanks Justin. I was told that the vdwtype = switch was an essential
component
:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Implementation and description of a model physics are two different
things. You could compute KE of a particle with 0.5 * m * v^2, but if
the mass is used nowhere else, why wouldn't you pre-multiply the mass
by 0.5?
Mark
On Wed, Sep 18
Look at the numbers, count the number of atoms you expect in each
moleculetype, and work out what the mismatch is.
Mark
On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl knnar...@sssihl.edu.in wrote:
Dear GMX users,
I am trying to simulate a protein in SDS/Water box.
1. No problems with
to change or comment out mdp options that are not
recognized by grompp. It is attached here. The simulation soon crashes with
LINCS errors after 25 steps, while the original tpr runs properly. I'm not
sure what's missing here.
On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.comwrote
Thanks for the follow up.
The take-home lesson is that building for BlueGene/Q is unlike
building for the usual homogenous x86 cluster. You still need an MPI
and non-MPI build, but the latter should be targeted at the front end
(Linux on PowerPC, usually), unless/until GROMACS tools acquire MPI
, Mark Abraham
mark.j.abra...@gmail.comwrote:
That -om mechanism has been broken for about a decade, unfortunately.
You will need to include the file, or post a link a file, not attach
it, if you want users of this list to see it.
gmxcheck to compare your new and old .tpr files is useful
wrote:
hmm, does that mean the gmx force field file format or specifications are
not backward compatible?
On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
There are technical differences between versions about how the VDW
parameters are computed. You should
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
the 3.x-era restart strategy when checkpoint files are unavailable.
But if you simply have no output files, then you have no ability to
restart.
Mark
On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
mahboobeh.esl...@yahoo.com
On Tue, Sep 17, 2013 at 2:04 AM, Kate Stafford kastaff...@gmail.com wrote:
Hi all,
I'm trying to install and test gromacs 4.6.3 on our new cluster, and am
having difficulty with MPI. Gromacs has been compiled against openMPI
1.6.5. The symptom is, running a very simple MPI process for any of
Standard error and standard deviation measure different things. Please
consult a general work on reporting scientific results.
Mark
On Mon, Sep 16, 2013 at 7:40 AM, afsaneh maleki
maleki.afsa...@gmail.com wrote:
Dear all
I would like to calculate the standard deviation (as the error bar)
Please answer all of Justin's questions. What is in the PDB file -
what should the C terminus be!
Mark
On Tue, Sep 17, 2013 at 2:27 AM, Santhosh Kumar Nagarajan
santhoshraja...@gmail.com wrote:
I have tried it Tsjerk.. But the same error is shown again..
-
Santhosh Kumar Nagarajan
MTech
there is no reason to change that).
Simply use md.cpt, now that you have it :-)
Mark
On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
mahboobeh.esl...@yahoo.com wrote:
I have md.cpt but I don't have restart my run
What is the purpose of the state.cpt file?
thank you so much
From: Mark Abraham mark.j.abra
much
- Forwarded Message -
From: Mark Abraham mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, September 17, 2013 11:22 AM
Subject: Re: [gmx-users] How to restart the crashed run
Hi,
Please keep discussion on the mailing list
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