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 no
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" wrote:
> Hello GROMACS users,
> I have phosphorylated Serine residue in my
> protein (140 residues) of
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, "Jhen
Hi,
Something went wrong earlier in your workflow. Check your log files, etc.
Mark
On Nov 13, 2013 3:57 AM, "guozhicheng222" wrote:
> Hi:
>
> When I am running the ibi procedure, I get the following error message:
>
>
>
> A coordinate in file conf.gro does
>
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 ru
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman 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?) AMD CPU
On Nov 10, 2013 10:04 AM, "Mark Abraham" 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.
On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling wrote:
> 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 many simulations wit
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 wrote:
> On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham >wrote:
>
> > Hi,
> >
> &g
vement?
>
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 >wrote:
>
> > You will do much b
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 wrote:
> Dear all,
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 trajectori
DGMX_MPI=ON
> -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF
> -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 Ab
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:
> Hell
wrote:
> 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 >wrote:
>
> > Hi,
> >
> > It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
> the
> >
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
wrote:
> Dear gromacs users
> I have installed gromacs 4.6.1 with cmake 2.8.12, fftw3.3.3 and
icc and CUDA is pretty painful. I'd suggest getting latest gcc.
Mark
On Thu, Nov 7, 2013 at 2:42 PM, 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
> correctly.
>
> I'm getting
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 a
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl 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
generate the compar
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.
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
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul 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 0.24 is
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 versi
Count the number of O observed near each C singly and compare the four
numbers.
Mark
On Nov 6, 2013 4:57 PM, "rankinb" 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 defined an
> inde
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" wrote:
> Hi Szilard,
>
> Thanks.
>
> >From Timo's benchmark,
> 1 node142 ns/day
> 2
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 wrote:
> Hi,
>
> I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having
> 32 processors (cpu). But whi
On Tue, Nov 5, 2013 at 12:55 PM, James Starlight wrote:
> 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 performation i
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta wrote:
> 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]# make
>
These is no
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" 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 help(the same as intro
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 wrote:
> i am a newbie
On Fri, Nov 1, 2013 at 4:04 AM, Xu Dong Huang 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 using
> g_bond be the
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati
wrote:
> 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 water). Again, dru
ut spamming the queue and yes
I
> will re-read PBS docs.
>
>
> On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham wrote:
>
> > On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty > >wrote:
> >
> > > Mark,
> > >
> > > The problem with one .tpr file se
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey 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 gives me 444.5 w
back its jobID. So I could submit
> job 5 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
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 bette
On Mon, Oct 28, 2013 at 7:56 PM, Xu Dong Huang wrote:
> Hello,
>
> I have couple objectives as part of an analysis of my simulated system.
> And I would like some opinions on the tools to use to achieve it.
>
> I have the following interest in my system:
> 1) Find the probability distribution (den
On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty wrote:
> 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 md_15
>
> This run
To make this clear, center the trajectory on the water and watch the time
evolution in some visualization program.
Mark
On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul wrote:
>
>
> On 10/27/13 12:05 PM, shahab shariati wrote:
>
>> Dear Tsjerk Wassenaar
>>
>> Very very thanks for your reply.
>>
On Sat, Oct 26, 2013 at 2:07 PM, Santu Biswas wrote:
> >
> >
> >
> > "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"
> wrote:
> >
> > > dear users,
> > >
> > > I am performing 500ps mdr
/Errors
> > -------
> >
> > "Hang On to Your Ego" (F. Black)
> >
> >
> >
>
> >
&g
On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes wrote:
> 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 = 16. Don´t know if
On Thu, Oct 24, 2013 at 6:24 PM, Corina Mo wrote:
> Dear Justin,
>
> Thanks again! Will look into it.
> Btw, you know if there is any plan to implement implicit lipid model in
> GROMACS?
>
No plans known.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/
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
wrote:
> Dear Mark
>
> Thank for your reply.
>
> If I show my system as 4 regions, my system before equilibration is
Ja. No twin-range => no long-range :-)
Mark
On Thu, Oct 24, 2013 at 5:50 PM, 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 happen.
>
> > Hi there,
On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner wrote:
> On Oct 24, 2013, at 4:25 PM, Mark Abraham
> wrote:
>
> > Hi,
> >
> > No. mdrun reports the stride with which it moves over the logical cores
> > reported by the OS, setting the affinity of GROMACS
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 an
"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" wrote:
> dear users,
>
> I am performing 500ps mdrun in vacuum for polypeptide(formed
> by 10-residues leucine) using gromacs_4.5.5(double-precision) us
On Oct 24, 2013 8:10 AM, "shahab shariati"
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 all lipid at
Center on a particular lipid? Or head group?
Mark
On Oct 23, 2013 6:13 PM, "shahab shariati"
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 bilayer
> membrane,
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,
opropylchloride
> is probably a liquid at 290K, if the model is parametrized reasonably.
> So it should not phase-separate.
>
> Vitaly
>
>
> On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham
> wrote:
> > On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" wrote:
> >>
On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" 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 to have occurre
On Oct 23, 2013 7:24 AM, "rajat desikan" 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 continuing thes
Probably, make your broken molecules whole before passing them to grompp.
Mark
On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar wrote:
> 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
> membrane simulations.
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 firs
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 wrote:
> Hi,
>
> I want to add chromium III ion into lipid bilayer. I have incl
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 >wrote:
>
> > Can this file be opened i
Can this file be opened in VMD itself?
Mark
On Oct 18, 2013 6:21 AM, "anu chandra" 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.
>
> #
4.5 can only handle about 500-1000 atoms per processor. Details vary.
Mark
On Oct 17, 2013 5:39 AM, "Nilesh Dhumal" 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, from the manua
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"
wrote:
> I have a system that also uses a set of distance restraints
>
> The box size is:
>7.12792 7.12792 10.25212
>
> When running mdrun -nt
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 Groma
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov 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 ./src/gmxlib/ |
(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 W
ark
Thanks again for your help!
>
> Best regards,
>
> James
>
>
> On 21 September 2013 23:12, Mark Abraham wrote:
>
> > On Sat, Sep 21, 2013 at 2:45 PM, James
> wrote:
> > > Dear Mark and the rest of the Gromacs team,
> > >
> > > Thanks
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" wrote:
>
>
> On 10/14/13 7:56 PM, Leandro Bortot wrote:
>
>> Dear GROMACS users,
>>
>> Does anyone know how significant is the difference between the
>> "origin
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
wrote:
> The barostat tries to equilibrate the system at the desired pressure, there
> will be
On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot <
guillaume.chev...@gmail.com> wrote:
> 2013/10/12 Mark Abraham
>
> > 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 larg
been mentioned:
> http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1
>
>
>
>
> 2013/10/11 Mark Abraham
>
> > On Oct 11, 2013 7:59 PM, "Guillaume Chevrot" <
> guillaume.chev...@gmail.com>
> > wrote:
> > >
> > > Hi all
On Oct 11, 2013 7:59 PM, "Guillaume Chevrot"
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 (see the attached
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 wrote:
> Dear Gromacs user,
> Can anyone tell me how to arrange for my login scripts to source gromacs
> automatically?
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 wrote:
> De
Great! Many thanks Justin, and the CHARMM team!
Mark
On Tue, Oct 8, 2013 at 10:16 PM, Justin Lemkul 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
> http://
link Mark sent you. Further
> up on the page is how you get started in terms of obtaining 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
>>
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
t-lambda-state from 0 to 8).
>
> gpc-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 (-:
>
&g
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 wrote:
> Unlikely possible... But yeah, the feature might be handy.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Thu, Sep 26, 2013 at 4:20 PM, grita wrote
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"
wrote:
> Dear Mark
>
> > The UNIX tool diff is your friend for comparing files.
>
> Thanks for your suggestion. I used diff and sdiff toll
> for comparing 2 files (
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
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 wrote:
> Dear GMXers,
> Since I am intereste
On Mon, Sep 23, 2013 at 8:08 PM, Szilárd Páll 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 simulations po
How do GAFF and acpype work?
Mark
On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong 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?
> --
> gmx-users mailin
On Sep 23, 2013 9:08 AM, "marzieh dehghan" 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 em.mdp -c test.
On Sep 23, 2013 9:23 AM, "Jonathan Saboury" 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 something e
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,
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury 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 the command
roceed further. Any help would be
> greatly appreciated.
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 fo
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 wrote:
> Hi Justin,
> Tha
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 wrote:
>
>
> On 9/19/13 9:55 PM, akk5r wrote:
>>
>> Thanks Justin. I was told that the "vdwtype = switch" was an essential
>> component of ru
The UNIX tool diff is your friend for comparing files.
On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati
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 the gro file before
On Thu, Sep 19, 2013 at 2:48 PM, Xu, Jianqing 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 jobs.
>
> Say I h
t; It is only a simple question, not a criticism of any kind. I'm sure there
> may be perfect reasons to choose one implementation over another. To
> someone who is not familiar with the history of gmx development, it is
> something to be aware of. That's all.
>
>
> On W
hat mean the gmx force field file format or specifications are
> not backward compatible?
>
>
> On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham wrote:
>
>> There are technical differences between versions about how the VDW
>> parameters are computed. You should not expec
gt;iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00
> idef->iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06
> idef->iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13
> idef->iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06
> idef->iparam[194]2: c6= 3.50750256e
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
fu
ut 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 wrote:
>
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 wrote:
> Dear GMX users,
>
> I am trying to simulate a protein in SDS/Water box.
>
> 1. No problems with pdb2gmx - .gro file and
No. Theoretically useful, but not implemented.
Mark
On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui
wrote:
> Thanks. Is it possible to dump the parameters in the tpr file to a mdp file?
>
>
> On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham wrote:
>
>> mdrun -nsteps in 4.6 ov
On Tue, Sep 17, 2013 at 5:31 PM, Christopher Neale
wrote:
> Dear Users:
>
> I am attempting to use the new BGQ kernels with the version of gromacs at
> https://gerrit.gromacs.org/#/c/2572/ , which I obtained by:
>
> git init
> git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 &&
mdrun -nsteps in 4.6 overrides the number of steps in the .tpr
Mark
On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
wrote:
> Dear GMX users,
>
> I'm new to Gromacs. So apologies if this question is too simple.
>
> I downloaded top/tpr files from the supplementary material of a published
> paper. T
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