Re: [gmx-users] local pressure
What are you looking for? Have a look at the papers they might be inspiring :)) On May 1, 2013, at 10:33 PM, Sikandar Mashayak symasha...@gmail.com wrote: Ok, I did rerun with local pressure mdrun, and got pressure.dat* files in binary format. how do I proceed from here? Any utility to analyze or post-process this? On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak symasha...@gmail.comwrote: Thanks Xavier, I will give it a try. On Wed, May 1, 2013 at 10:56 AM, XAvier Periole x.peri...@rug.nl wrote: Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are :)). The paper related to the use would be: Ollila et al, PRL 102, 078101 (2009) Ollila et al, Biophysical Journal (100)1651–59 On May 1, 2013, at 5:48 PM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Xavier Can you please elaborate on how to use and post-process the local pressure version of gromacs? Do you have any examples or reference article? May be you can create a HowTo wiki as Justin suggested, it would be of great help. Thanks Sikandar On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/1/13 5:12 AM, XAvier Periole wrote: The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. That would be a great topic for a wiki How-To. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. I never said it would go away, but given the fact that there have been no updates to the git branch in over 3 years, it's simply unlikely that anyone has cared to move it forward. If someone wants to update the code to be compatible with 4.6, that would be a welcome contribution. Lack of any request for improvements and inclusion in an official release has likely led to the decline in interest from the development team. If you want something included, you should file a feature request on redmine.gromacs.org - it's the only official way we keep track of fixes and features. If it's not there, it likely won't get addressed until one of the developers has a compelling need to work on it. -Justin On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/**projects/gromacs/repository/** show?rev=localpressure-4-0 http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 . I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post
Re: [gmx-users] g_msd for many molecules
Thanks for this Vitaly and Justin. George The resulting MSD will correspond to the average from individual atoms. Calculating MSD of an individual atom and ascribing it to a [small] molecule, which this atom belongs to, is reasonable. Assuming that averaged MSD from atoms correspond to the cluster they form is not. Dr. Vitaly Chaban On Wed, May 1, 2013 at 2:40 PM, George Patargias g...@bioacademy.gr wrote: Hello I am trying to calculate the MSD of 8 molecules in a lipid bilayer with g_msd. If I include the atoms of all these 8 molecules as a single group in the index file, will g_msd calculate the MSD of the center of mass of them or it will average over all atoms? Thanks George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: local pressure
Hi everybody, There is some more information about the issue in the MARTINI web page: http://md.chem.rug.nl/cgmartini/index.php/3d From there you can download the tools to analyze the binary file localpressure.dat which is given out by a gromacs code. There is more information in the README file in the pressure-tools package and also in the publications [1,2,3,4]. I have tested the version linked in the MARTINI page pretty widely against independently written code and the results are the same, thus I think it is pretty reliable. I know that there exist also a version for 4.5. since some people have asked me about the results they have calculated with that. Based on those discussions I have got an impression that the version for 4.5. gives different results than the version linked in the MARTINI page. However, I have not tested the version for 4.5. myself and I do not have it. I do get questions related to the pressure profile calculations monthly and the paper reperesenting the methos for 3D calculations [1] also gets regularly cited (44 total, 13 this year) so I think that there is some interest on this issue. Also several people have been able to perform these calculations so it is doable. Since the code is ment to work as rerun analysis, one can split the trajectory in the pieces and separately analyze them (trivial parallelization). This helps if the code is too slow. [1] Ollila et al. PRL 102: 078101 (2009) [2] Ollila et al. Biophysical Journal, Volume 100, Issue 7, 1651-1659 (2011) [3] Ollila et al. Biophysical Journal, Volume 103, Issue 6, 1236-1244 (2012) [4] Ollila PHD thesis, http://dspace.cc.tut.fi/dpub/handle/123456789/6813 BR, Samuli Ollila -- View this message in context: http://gromacs.5086.x6.nabble.com/local-pressure-tp5007803p5007844.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_msd for many molecules
Hi,
if you want to calculate the MSD of several molecules, say nrmol, without
using the
-mol option, which I do not know is still broken, you can do this in
three simple steps:
1. Convert your trajectory with trjconv and the option -pbc whole
2. Create an index file, that contains groups, which contain one
molecule each, and remove the standard groups like System ...
3. run the analysis with: echo {0..nrmol} | g_msd -f convertedtrajecotry
-n indexfile -ng nrmol
This gives you the correct MSD for the center of mass for every
molecule.
Cheers,
Flo
* George Patargias g...@bioacademy.gr [2013-05-02 10:08:20 +0300]:
Thanks for this Vitaly and Justin.
George
The resulting MSD will correspond to the average from individual atoms.
Calculating MSD of an individual atom and ascribing it to a [small]
molecule, which this atom belongs to, is reasonable. Assuming that
averaged
MSD from atoms correspond to the cluster they form is not.
Dr. Vitaly Chaban
On Wed, May 1, 2013 at 2:40 PM, George Patargias g...@bioacademy.gr
wrote:
Hello
I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
g_msd. If I include the atoms of all these 8 molecules as a single group
in the index file, will g_msd calculate the MSD of the center of mass of
them or it will average over all atoms?
Thanks
George
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Institute for Computational Physics
University Stuttgart
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RE: [gmx-users] help with g_hydorder and g_polystat
That's ok. Thank you for your help. In the meantime, I might see if g_h2order is a good substitute for g_hydorder. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 01 May 2013 22:58 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 5/1/13 8:44 AM, Emmanuel, Alaina wrote: No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same. When I use g_polystat, I use the following command: g_polystat_d -f file.xtc -s file.tpr -n polymer_backbone.ndx -p persist.xvg -o polystat.xvg Note: Using polymer_backbone.ndx yields fewer polymers with nan issues, than using the whole polymer structure in an index file. The g_hydorder problem is a bug in the code and I have filed a bug report on Redmine. I have no insight into what's going on with g_polystat, sorry. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] minimization of particular residue/atom
Dear Mark, I found a simple(est) fix to this problem. Say in my case I was getting error inf on atom 4281 ( Maximum force =inf on atom 4281) What I did: In gro file for atom number 4281 I edited one of its coordinate just 0.1nm that is 1 Angs e.g. 6.518 to 6.618 (I did for x, but can be y or z). So mdrun was complaining one by one and I edited in all three such x coordinates for three atoms. finally I was able to achieve convergence. I believe moving just 0.1 nm minimization will take care of correct lengths. May be if its not the correct way; please suggest. regards, On Thu, May 2, 2013 at 12:50 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, May 1, 2013 at 4:20 PM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I am using Charmm gui built membrane (120 x 2). But during minimization I was getting error. Potential Energy = 4.6809051e+19 Maximum force =inf on atom 4281 Norm of force =inf (inf means? means infinite/NAN) All the above means your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up I removed the full lipid residue having atom number 4281. I was again getting error representing some other atoms so finally I removed three lipid residues. Doing this I was able to complete convergence. I have two queries: 1) As I have removed three residues from Charmm gui membrane, does this affect final results? Although I will be doing MD for membrane first. Maybe. We don't know whether the membrane was built wrongly, or you post-processed the coordinate file wrongly, or whether you need all the lipid molecules to achieve the right density, or... 2) Also is there any way so that particular atoms can be minimized or ''touched'' ? Here in this case I removed three lipid residues but this will not be good say in case of proteins. Just as a analogy if this problem arises in AMBER (rather I faced such problem many times) I can use xleap and can move atom a little and relax it particularly by selecting it , so that later if use the edited structure I get convergence properly without error. You can only do that by moving the coordinates by hand in the coordinate file before you give it to grompp. Your PE above is so large that this is not the right approach to fix the problem. I would guess your periodic box is not the one you were intended to use. Mark regards, Jio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: PMF calculation between protein and ligand
If you refer to Justin's tutorial, you can use it for every system, where the reaction coordinate is the distane between two parts of the system. You probably need to make some little adjustments, but in the end it doesn't matter if you pull two proteins apart, or protein+ligand, 2 water molecules, or even streth a protein. Greetings Thomas Am 02.05.2013 08:59, schrieb gmx-users-requ...@gromacs.org: Sir I have query as to how to go ahead for potential mean force (PMF) calculation between protein and ligand. As per the umbrella sampling protocol you have provided us in gromacs tutotrial it says it is for protein molecules... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] minimization of particular residue/atom
That procedure can work. That it works in your case surprises me a little. :-) Mark On Thu, May 2, 2013 at 11:25 AM, gromacs query gromacsqu...@gmail.comwrote: Dear Mark, I found a simple(est) fix to this problem. Say in my case I was getting error inf on atom 4281 ( Maximum force =inf on atom 4281) What I did: In gro file for atom number 4281 I edited one of its coordinate just 0.1nm that is 1 Angs e.g. 6.518 to 6.618 (I did for x, but can be y or z). So mdrun was complaining one by one and I edited in all three such x coordinates for three atoms. finally I was able to achieve convergence. I believe moving just 0.1 nm minimization will take care of correct lengths. May be if its not the correct way; please suggest. regards, On Thu, May 2, 2013 at 12:50 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 1, 2013 at 4:20 PM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I am using Charmm gui built membrane (120 x 2). But during minimization I was getting error. Potential Energy = 4.6809051e+19 Maximum force =inf on atom 4281 Norm of force =inf (inf means? means infinite/NAN) All the above means your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up I removed the full lipid residue having atom number 4281. I was again getting error representing some other atoms so finally I removed three lipid residues. Doing this I was able to complete convergence. I have two queries: 1) As I have removed three residues from Charmm gui membrane, does this affect final results? Although I will be doing MD for membrane first. Maybe. We don't know whether the membrane was built wrongly, or you post-processed the coordinate file wrongly, or whether you need all the lipid molecules to achieve the right density, or... 2) Also is there any way so that particular atoms can be minimized or ''touched'' ? Here in this case I removed three lipid residues but this will not be good say in case of proteins. Just as a analogy if this problem arises in AMBER (rather I faced such problem many times) I can use xleap and can move atom a little and relax it particularly by selecting it , so that later if use the edited structure I get convergence properly without error. You can only do that by moving the coordinates by hand in the coordinate file before you give it to grompp. Your PE above is so large that this is not the right approach to fix the problem. I would guess your periodic box is not the one you were intended to use. Mark regards, Jio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote:
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
first sign is a huge jump in LJ interactions and pressure. This jump seems
to be absorbed by the box size and temperature when possible … see example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually
got worse. I was able to run a 500 ns simulation with gmx405 using similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem …
one exchange is not properly done at the second trial, while the first ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
OK, thanks for the effort. That all agrees with my suspicion that the full
state is not being exchanged.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not going
across but it might be something completely different, when the consecutive
systems differ reasonably.
I've never tried, but an experiment with a water box might be instructive.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
There is an outstanding REMD issue on redmine that could be related (
http://redmine.gromacs.org/issues/1191). I'd suggest you open a new issue
there, upload a minimal set of .tprs that can reproduce the problem and
anything you can think of that might help investigate. For something I'm
doing, I'd like to be sure the full T-coupling state is being exchanged,
and we may as well kill all the bugs at once.
Mark
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b, state-svir_prev, DIM);
exchange_rvecs(ms, b, state-fvir_prev, DIM);
exchange_rvecs(ms, b, state-pres_prev, DIM);
exchange_doubles(ms, b, state-nosehoover_xi, ngtc);
exchange_doubles(ms, b, state-nosehoover_vxi, ngtc);
exchange_doubles(ms, b, state-nhpres_xi, nnhpres);
Re: [gmx-users] issue in replica exchange
I'm running remd in NPT ensemble for a small peptide and all is ok if the
maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat
and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to
1bar. Gromacs version 4.5.5. Exchange trials every 5 ps.
If I try to add replica at a higher temperature the system crash, but I
think it is a problem of equilibration.
2013/5/1 XAvier Periole x.peri...@rug.nl
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
first sign is a huge jump in LJ interactions and pressure. This jump seems
to be absorbed by the box size and temperature when possible … see example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually
got worse. I was able to run a 500 ns simulation with gmx405 using similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem …
one exchange is not properly done at the second trial, while the first ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not going
across but it might be something completely different, when the consecutive
systems differ reasonably.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b, state-svir_prev, DIM);
exchange_rvecs(ms, b, state-fvir_prev, DIM);
exchange_rvecs(ms, b, state-pres_prev, DIM);
exchange_doubles(ms, b, state-nosehoover_xi, ngtc);
exchange_doubles(ms, b, state-nosehoover_vxi, ngtc);
exchange_doubles(ms, b, state-nhpres_xi, nnhpres);
exchange_doubles(ms, b, state-nhpres_vxi, nnhpres);
exchange_doubles(ms, b, state-therm_integral, state-ngtc);
exchange_rvecs(ms, b, state-x, state-natoms);
exchange_rvecs(ms, b, state-v, state-natoms);
exchange_rvecs(ms, b,
Re: [gmx-users] issue in replica exchange
Did you look at some data like temperature/pressure/box size/Epot as a function
of time and especially around some exchanges?
Your system is atomistic I presume.
On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote:
I'm running remd in NPT ensemble for a small peptide and all is ok if the
maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat
and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to
1bar. Gromacs version 4.5.5. Exchange trials every 5 ps.
If I try to add replica at a higher temperature the system crash, but I
think it is a problem of equilibration.
2013/5/1 XAvier Periole x.peri...@rug.nl
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
first sign is a huge jump in LJ interactions and pressure. This jump seems
to be absorbed by the box size and temperature when possible … see example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually
got worse. I was able to run a 500 ns simulation with gmx405 using similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem …
one exchange is not properly done at the second trial, while the first ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not going
across but it might be something completely different, when the consecutive
systems differ reasonably.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b, state-svir_prev, DIM);
exchange_rvecs(ms, b, state-fvir_prev, DIM);
exchange_rvecs(ms, b, state-pres_prev, DIM);
exchange_doubles(ms, b, state-nosehoover_xi, ngtc);
exchange_doubles(ms, b, state-nosehoover_vxi, ngtc);
exchange_doubles(ms, b, state-nhpres_xi, nnhpres);
exchange_doubles(ms, b,
Re: [gmx-users] issue in replica exchange
I saw that redmine report, which could be related but it seems to happen only
for runs done outside the domain and particle decompositions.
I'll fill up a red mine.
Anything I could do to help speeding the fix?
On May 2, 2013, at 11:53 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote:
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
first sign is a huge jump in LJ interactions and pressure. This jump seems
to be absorbed by the box size and temperature when possible … see example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually
got worse. I was able to run a 500 ns simulation with gmx405 using similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem …
one exchange is not properly done at the second trial, while the first ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
OK, thanks for the effort. That all agrees with my suspicion that the full
state is not being exchanged.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not going
across but it might be something completely different, when the consecutive
systems differ reasonably.
I've never tried, but an experiment with a water box might be instructive.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
There is an outstanding REMD issue on redmine that could be related (
http://redmine.gromacs.org/issues/1191). I'd suggest you open a new issue
there, upload a minimal set of .tprs that can reproduce the problem and
anything you can think of that might help investigate. For something I'm
doing, I'd like to be sure the full T-coupling state is being exchanged,
and we may as well kill all the bugs at once.
Mark
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b,
Re: [gmx-users] Temperature for individual amino acid residues
On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] surrounding a peptide by ions of magnesium
On 5/2/13 12:38 AM, Mohan maruthi sena wrote: Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we have 0.5 Molar Mg+2 solution, My question how can find concentration by increasing number of ions. I don't fully understand what you're trying to do, especially in the absence of solvent, but I'll venture some simple advice. Concentration is just the number of moles per unit volume. Simple unit conversion exercises will tell you how many ions are needed to achieve whatever target concentration you're looking for. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] surrounding a peptide by ions of magnesium
Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? Thanks, Mohan On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 12:38 AM, Mohan maruthi sena wrote: Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we have 0.5 Molar Mg+2 solution, My question how can find concentration by increasing number of ions. I don't fully understand what you're trying to do, especially in the absence of solvent, but I'll venture some simple advice. Concentration is just the number of moles per unit volume. Simple unit conversion exercises will tell you how many ions are needed to achieve whatever target concentration you're looking for. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] surrounding a peptide by ions of magnesium
On 5/2/13 7:33 AM, Mohan maruthi sena wrote: Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? genbox -ci -nmol You will need a coordinate file for a single Mg2+ ion to be inserted, which is trivial to create by hand. I don't know how the ion force field parameters will behave in the absence of explicit solvent. Are you planning to use implicit solvent? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Yes, my system is described at atomic level.
No, I can't see any strange value around exchanges. I analyzed only a
very little number of trajectories, but temperature, volume, potential
energy, pressure seem all to be around normal fluctuations.
2013/5/2 XAvier Periole x.peri...@rug.nl
Did you look at some data like temperature/pressure/box size/Epot as a
function of time and especially around some exchanges?
Your system is atomistic I presume.
On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote:
I'm running remd in NPT ensemble for a small peptide and all is ok if the
maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat
and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals
to
1bar. Gromacs version 4.5.5. Exchange trials every 5 ps.
If I try to add replica at a higher temperature the system crash, but I
think it is a problem of equilibration.
2013/5/1 XAvier Periole x.peri...@rug.nl
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the
swap,
first sign is a huge jump in LJ interactions and pressure. This jump
seems
to be absorbed by the box size and temperature when possible … see
example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might
actually
got worse. I was able to run a 500 ns simulation with gmx405 using
similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself
(externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at
first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in
2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT
REMD
simulation after equilibration in the same NVT ensemble (for 1 ns)
removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the
problem …
one exchange is not properly done at the second trial, while the first
ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving,
meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be
fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my
system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not
going
across but it might be something completely different, when the
consecutive
systems differ reasonably.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b,
Re: [gmx-users] issue in replica exchange
Could you send me a set of tar files that I could look at things the same way I do with my system? I would guess that 6 tar files where you same energies and print log file every step but xtc and trr files not that often would be really cool. You can send them directly to my email (x.peri...@rug.nl) unless they are too big. If you do not like the idea it is also ok. On May 2, 2013, at 1:38 PM, Simone Conti simone...@gmail.com wrote: Yes, my system is described at atomic level. No, I can't see any strange value around exchanges. I analyzed only a very little number of trajectories, but temperature, volume, potential energy, pressure seem all to be around normal fluctuations. 2013/5/2 XAvier Periole x.peri...@rug.nl Did you look at some data like temperature/pressure/box size/Epot as a function of time and especially around some exchanges? Your system is atomistic I presume. On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote: I'm running remd in NPT ensemble for a small peptide and all is ok if the maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. If I try to add replica at a higher temperature the system crash, but I think it is a problem of equilibration. 2013/5/1 XAvier Periole x.peri...@rug.nl Ok here is my current status on that REMD issue. For info: I use Temperature: v-rescale, tau_t = 2.0 ps Pressure: berendsen, tau_p = 5.0 ps, time step: dt=0.002 - 0.020 fs, COM removal on for bilayer/water separately The symptoms: explosion of the system after 2-5 steps following the swap, first sign is a huge jump in LJ interactions and pressure. This jump seems to be absorbed by the box size and temperature when possible … see example I provided earlier. A large VCM (velocity centre of mass?) is often associated with the crash. But also pressure scaling more than 1% ... 1- the problem mentioned above remains in gmx-4.5.7 and it might actually got worse. I was able to run a 500 ns simulation with gmx405 using similar setup as for gmx457. The following point happened in gmx457. 2- it persists with a time step of 2 fs. Actually all tests performed in the following used dt=2fs. 3- if I perform an exchange that explodes within mdrun myself (externally to the remd gromacs by getting the gro file with the mdp adjusting the temperature) it goes all fine. 4- the issue gets much worst when the consecutive replicas differ (different protein conformations and the box size etc) … explosion at first exchange. 5- the use of parrinelo-raman does not help 6- cancelling the centre of mass removal does not remove the problem. 7- switching to NVT ensemble does not help but makes it worst (crash in 2 steps). All exchanges accepted at first attempt crash with the message Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX 8- using a unique conformation (the same) for all replicas in the NVT REMD simulation after equilibration in the same NVT ensemble (for 1 ns) removes the problem. 9- taking the equilibrated NVT conformations, equilibrate them in an NPT ensemble (1 ns) and let go the exchanges afterwards restores the problem … one exchange is not properly done at the second trial, while the first ones were fine. Well if errors were made that was with reasonable 10- note also that the coarse grain I use is extremely forgiving, meaning you can perform really nasty transformations and run it further after simple minimisation … so even abrupt changes in temperatures should be fine and relax quickly. 11- when looking at the conformations themselves nothing appears to have jumped over or nothing funky. At this point I am not sure what to think and what to do next. There is definitely something not going right during the exchanges. Anyone has been able to run a REMD simulation in an NPT ensemble without crashes? I would imagine someone has and something particular to my system is making it going wrong but I am really wondering what it could be. My feeling is that something relative to the box size or pressure is not going across but it might be something completely different, when the consecutive systems differ reasonably. However that would suggest that the manner the exchanges are made is severely wrong in some cases. Any help to resolve the problem would be greatly appreciated. XAvier. On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote: Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble data. The coupling to P and T and not exchanged with it? The code in src/kernel/repl_ex.c: static void exchange_state(const
Re: [gmx-users] issue in replica exchange
I mean tpr files not tar! Autocorrection is sometimes funny :)) On May 2, 2013, at 2:11 PM, XAvier Periole x.peri...@rug.nl wrote: Could you send me a set of tar files that I could look at things the same way I do with my system? I would guess that 6 tar files where you same energies and print log file every step but xtc and trr files not that often would be really cool. You can send them directly to my email (x.peri...@rug.nl) unless they are too big. If you do not like the idea it is also ok. On May 2, 2013, at 1:38 PM, Simone Conti simone...@gmail.com wrote: Yes, my system is described at atomic level. No, I can't see any strange value around exchanges. I analyzed only a very little number of trajectories, but temperature, volume, potential energy, pressure seem all to be around normal fluctuations. 2013/5/2 XAvier Periole x.peri...@rug.nl Did you look at some data like temperature/pressure/box size/Epot as a function of time and especially around some exchanges? Your system is atomistic I presume. On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote: I'm running remd in NPT ensemble for a small peptide and all is ok if the maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. If I try to add replica at a higher temperature the system crash, but I think it is a problem of equilibration. 2013/5/1 XAvier Periole x.peri...@rug.nl Ok here is my current status on that REMD issue. For info: I use Temperature: v-rescale, tau_t = 2.0 ps Pressure: berendsen, tau_p = 5.0 ps, time step: dt=0.002 - 0.020 fs, COM removal on for bilayer/water separately The symptoms: explosion of the system after 2-5 steps following the swap, first sign is a huge jump in LJ interactions and pressure. This jump seems to be absorbed by the box size and temperature when possible … see example I provided earlier. A large VCM (velocity centre of mass?) is often associated with the crash. But also pressure scaling more than 1% ... 1- the problem mentioned above remains in gmx-4.5.7 and it might actually got worse. I was able to run a 500 ns simulation with gmx405 using similar setup as for gmx457. The following point happened in gmx457. 2- it persists with a time step of 2 fs. Actually all tests performed in the following used dt=2fs. 3- if I perform an exchange that explodes within mdrun myself (externally to the remd gromacs by getting the gro file with the mdp adjusting the temperature) it goes all fine. 4- the issue gets much worst when the consecutive replicas differ (different protein conformations and the box size etc) … explosion at first exchange. 5- the use of parrinelo-raman does not help 6- cancelling the centre of mass removal does not remove the problem. 7- switching to NVT ensemble does not help but makes it worst (crash in 2 steps). All exchanges accepted at first attempt crash with the message Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX 8- using a unique conformation (the same) for all replicas in the NVT REMD simulation after equilibration in the same NVT ensemble (for 1 ns) removes the problem. 9- taking the equilibrated NVT conformations, equilibrate them in an NPT ensemble (1 ns) and let go the exchanges afterwards restores the problem … one exchange is not properly done at the second trial, while the first ones were fine. Well if errors were made that was with reasonable 10- note also that the coarse grain I use is extremely forgiving, meaning you can perform really nasty transformations and run it further after simple minimisation … so even abrupt changes in temperatures should be fine and relax quickly. 11- when looking at the conformations themselves nothing appears to have jumped over or nothing funky. At this point I am not sure what to think and what to do next. There is definitely something not going right during the exchanges. Anyone has been able to run a REMD simulation in an NPT ensemble without crashes? I would imagine someone has and something particular to my system is making it going wrong but I am really wondering what it could be. My feeling is that something relative to the box size or pressure is not going across but it might be something completely different, when the consecutive systems differ reasonably. However that would suggest that the manner the exchanges are made is severely wrong in some cases. Any help to resolve the problem would be greatly appreciated. XAvier. On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote: Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble
Re: [gmx-users] issue in replica exchange
On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] vacum simulation
Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] vacum simulation
On 5/2/13 8:40 AM, Souilem Safa wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? http://www.gromacs.org/Documentation/Terminology/Blowing_Up Probably something is wrong in your topology or .mdp file, but since you've provided neither, it's hard to provide any specific advice. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] vacum simulation
You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters. Erik On 2 May 2013, at 14:40, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] vacum simulation
Thank you for your quick answer I have joined here my mdp file and the toplogy one also. Should I increase the time step? I'm sorry I'm new in MD On 2 May 2013 21:48, Erik Marklund er...@xray.bmc.uu.se wrote: You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters. Erik On 2 May 2013, at 14:40, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] vacum simulation
On 5/2/13 8:57 AM, Souilem Safa wrote: Thank you for your quick answer I have joined here my mdp file and the toplogy one also. The mailing list does not accept attachments. Please copy and paste the text into an email. We may not need the whole topology, but a description of what you're working with is important. If you are using some novel molecule for which you've generated parameters, those can be a source of problems. Should I increase the time step? I'm sorry I'm new in MD Increasing the timestep in the case of instabilities is the exact opposite of what you should do. Please read the link I posted earlier. -Justin On 2 May 2013 21:48, Erik Marklund er...@xray.bmc.uu.se wrote: You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters. Erik On 2 May 2013, at 14:40, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] vacum simulation
Thank you very much On 2 May 2013 22:00, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 8:57 AM, Souilem Safa wrote: Thank you for your quick answer I have joined here my mdp file and the toplogy one also. The mailing list does not accept attachments. Please copy and paste the text into an email. We may not need the whole topology, but a description of what you're working with is important. If you are using some novel molecule for which you've generated parameters, those can be a source of problems. Should I increase the time step? I'm sorry I'm new in MD Increasing the timestep in the case of instabilities is the exact opposite of what you should do. Please read the link I posted earlier. -Justin On 2 May 2013 21:48, Erik Marklund er...@xray.bmc.uu.se wrote: You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters. Erik On 2 May 2013, at 14:40, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] Temperature for individual amino acid residues
Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. N is the total number of protein atoms and Ncons will be equal to total number of constrains. 1) Do we have to take total numbers of pairs mentioned in .top file as a Ncons ( I am using all-bonds constraints in mdp file) ? 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature for individual amino acid residues
On 5/2/13 10:28 AM, bipin singh wrote: Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. N is the total number of protein atoms and Ncons will be equal to total number of constrains. N = number of atoms in the group being analyzed Ncons = number of constraints in that same group 1) Do we have to take total numbers of pairs mentioned in .top file as a Ncons ( I am using all-bonds constraints in mdp file) ? Pairs have nothing to do with degrees of freedom. 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? I guess that depends on what you want to observe, but multiplying each frame's value by a constant and then averaging gives the same as averaging and multiplying by a constant. -Justin On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature for individual amino acid residues
On 5/2/13 10:28 AM, bipin singh wrote: Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. N is the total number of protein atoms and Ncons will be equal to total number of constrains. N = number of atoms in the group being analyzed Ncons = number of constraints in that same group 1) Do we have to take total numbers of pairs mentioned in .top file as a Ncons ( I am using all-bonds constraints in mdp file) ? Pairs have nothing to do with degrees of freedom. 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? There is no single value; each group analyzed will have its own scaling factor. Use of the scaling factor depends on what you want to observe, but multiplying each frame's value by a constant and then averaging gives the same as averaging and multiplying by a constant, so you might save yourself some work if you just care about averages. -Justin On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Exdending
Dear Gromacs Community, I m in the situation where I have a trajectory that started in a geometric position A and ended in position B. If I hit a new mdrun with the -append extension, than the trr output is the old trajectory together with the new one which starts at position B. Unfortunately I want the new trr output to be the old trajectory together with the new one which should start again at position A. The new trajectory should differ from the old one, since I have random seed on. My question is, how do I get gromacs to do that? Is it enough if I just don't pass a Checkpoint file, or should I construct a checkpointfile from the first frame? To get a checkpointfile from the first frame I guess I have to start a trajectory with 1 timestep - or is there a smarter way? Thank you guys and sorry for my english, best regards, Dubi -- View this message in context: http://gromacs.5086.x6.nabble.com/Exdending-tp5007871.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Exdending
On 5/2/13 11:01 AM, Dubi wrote: Dear Gromacs Community, I m in the situation where I have a trajectory that started in a geometric position A and ended in position B. If I hit a new mdrun with the -append extension, than the trr output is the old trajectory together with the new one which starts at position B. Unfortunately I want the new trr output to be the old trajectory together with the new one which should start again at position A. The new trajectory should differ from the old one, since I have random seed on. My question is, how do I get gromacs to do that? Is it enough if I just don't pass a Checkpoint file, or should I construct a checkpointfile from the first frame? To get a checkpointfile from the first frame I guess I have to start a trajectory with 1 timestep - or is there a smarter way? You can't build a new checkpoint file like that. It sounds to me like you just need to run a new simulation. Setting gen_seed = -1 generates a random seed for velocities, but those velocities are then stored in the .tpr file; they are not re-generated randomly when mdrun begins. I think what you need to do is just run a new simulation. If you want to append it to your existing .trr file (for whatever reason), that's what trjcat is for. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] where can be obtain circled lipids bilayer?
Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where can be obtain circled lipids bilayer?
On Thu, May 2, 2013 at 6:32 PM, Albert mailmd2...@gmail.com wrote: Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~**ggroenh/membed/vesicle.pnghttp://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png 1) When packing parameter of the the lipid is large enough. 2) When concentration of lipids in the box is reasonably low. Dr. Vitaly Chaban thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] vacum simulation
LINCS doesn't like your system... or your system doesn't like LINCS... You can decrease the time-step as the simplest action. Dr. Vitaly Chaban On Thu, May 2, 2013 at 2:40 PM, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPU job often stopped
the problem is still there... :-( On 04/29/2013 06:06 PM, Szilárd Páll wrote: On Mon, Apr 29, 2013 at 3:51 PM, Albertmailmd2...@gmail.com wrote: On 04/29/2013 03:47 PM, Szilárd Páll wrote: In that case, while it isn't very likely, the issue could be caused by some implementation detail which aims to avoid performance loss caused by an issue in the NVIDIA drivers. Try running with the GMX_CUDA_STREAMSYNC environment variable set. Btw, were there any other processes using the GPU while mdrun was running? Cheers, -- Szilárd thanks for kind reply. There is no any other process when I am running Gromacs. do you mean I should set GMX_CUDA_STREAMSYNC in the job script like: export GMX_CUDA_STREAMSYNC=/opt/cuda-5.0 Sort of, but the value does not matter. So if your shell is bash, the above as well as simply export GMX_CUDA_STREAMSYNC= will work fine. Let us know if this avoided the crash - when you have simulated long enough to be able to judge. Cheers, -- Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where can be obtain circled lipids bilayer?
The shape is a sphere not a circle, what the picture is showing is a cut through the vesicle. Have you googled lipid vesicles? I don't know of a place that will have template systems like this for you. But you should be able to get these by making a large enough system with enough lipids to form the vesicle. Equilibration time might be a bit long. But maybe somebody will chime in who has a template system you can get... Best, Jesper On May 2, 2013, at 9:32 AM, Albert mailmd2...@gmail.com wrote: Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where can be obtain circled lipids bilayer?
On 5/2/13 2:16 PM, Jesper Sørensen wrote: The shape is a sphere not a circle, what the picture is showing is a cut through the vesicle. Have you googled lipid vesicles? I don't know of a place that will have template systems like this for you. But you should be able to get these by making a large enough system with enough lipids to form the vesicle. Equilibration time might be a bit long. But maybe somebody will chime in who has a template system you can get... Packmol can build such systems. They have an example online: http://www.ime.unicamp.br/~martinez/packmol/examples/ -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Some good news … The tpr files provided by Simone do NOT show abnormal behaviour! This good news :)) However after turning ON the particle decomposition option to mdrun (-pd) I got a warnings of water not being able to be settled and a crash. This was still with Simone's trips … I took that as a good sign! Then I went back to my system and changed the topology to be able to turn OFF the particle decomposition that I need to use due to a long bond … the system when right trough 650 ps with many exchanges without a complain. I would have to check the continuity in the energies, Temp and other but it seems to be quite clear: The problem I am facing is located in the particle decomposition section of the code. I will fill a redmine and let see how to proceed from there. I won't be able to do this before middle of next week though. Tks for your help, XAvier. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] where can be obtain circled lipids bilayer?
On 02.05.2013 18:32, Albert wrote: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png As has already been said by others, this is not really a circled lipid bilayer but rather a lipid vesicle of very very small size (maybe 10nm-15nm diameter, guessing from the layer thickness). There are indeed circular lipid bilayer structures possible, but they are not found very frequently. See here for example: Seifert, U. Vesicles of toroidal topology. Phys Rev Lett 1991, 66 :2404-2407 Fourcade, B., Mutz, M., Bensimon, D. Experimental and theoretical study of toroidal vesicles. Phys Rev Lett 1992, 68:2551-2554 To build a (spehrical) vesicle, you would usually start from one lipid molecule of your choice, which can be downloaded from one of the lipid libraries (e.g: http://www.nyu.edu/pages/mathmol/library/lipids/ or elsewhere). You'd rotate that in some way, maybe oriented parallel to the z axis of your coordinate system. After this, you write a small script which creates points distributed on an outer sphere (outer vesicle layer) and on an inner sphere (inner vesicle layer) separated by the length of about two molecules. On these points, you'd copy your single molecule, rotated by the angles of your z axis to the direction of the point. For the inner sphere, you'd add another 180° (wo that the lipid tails point inwards). Thats it. This structure has to be minimized and then simulated with caution (means: a very small time step for the first round). M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
So to summarize -- the problem appears to be with particle decomposition. On Thu, May 2, 2013 at 4:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
[gmx-users] constant protonation state MD
Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance of pull group 1 is larger than the box size
Hello sir I got the following error while running pulling mdrun -s pull.tpr distance of pull group 1 is larger than the box size I request you to kindly guide me in overcoming the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Are confirming that you reproduce the problem with gmx-4.6.1 or simply summarizing in case we lose track :)) On May 2, 2013, at 23:31, Michael Shirts mrshi...@gmail.com wrote: So to summarize -- the problem appears to be with particle decomposition. On Thu, May 2, 2013 at 4:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] vacum simulation
many thanks to all of you. I have decreased the time step. Simulation has finished in right conditions On 3 May 2013 03:06, Dr. Vitaly Chaban vvcha...@gmail.com wrote: LINCS doesn't like your system... or your system doesn't like LINCS... You can decrease the time-step as the simplest action. Dr. Vitaly Chaban On Thu, May 2, 2013 at 2:40 PM, Souilem Safa safasouil...@gmail.com wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] Temperature for individual amino acid residues
Thanks for your reply and suggestions. On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 10:28 AM, bipin singh wrote: Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. N is the total number of protein atoms and Ncons will be equal to total number of constrains. N = number of atoms in the group being analyzed Ncons = number of constraints in that same group 1) Do we have to take total numbers of pairs mentioned in .top file as a Ncons ( I am using all-bonds constraints in mdp file) ? Pairs have nothing to do with degrees of freedom. 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? There is no single value; each group analyzed will have its own scaling factor. Use of the scaling factor depends on what you want to observe, but multiplying each frame's value by a constant and then averaging gives the same as averaging and multiplying by a constant, so you might save yourself some work if you just care about averages. -Justin On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/pipermail/gmx-users/2003- March/004870.htmlhttp://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.html http://**lists.gromacs.org/pipermail/**gmx-users/2003-March/004870.** htmlhttp://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] rotation of a ligand
Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which tool should I use? g_order, g_chi, g_dih? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
