Re: [gmx-users] Doubt about the Gromacs versions
Thanks for the clarification. On Thu, Apr 25, 2013 at 7:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/13 9:48 AM, Richard Broadbent wrote: The 4.6.1 release is a more advanced version of gromacs with the latest kernels and features (GPU support, verlet cut-offs etc.). 4.5.7 is a maintenance release for those of us who for whatever reason wish to keep using the older 4.5.x series release. It mainly adds fixes made to the 4.6.x series to the 4.5.x version of the code. I use it as most of my calculations were conducted in 4.5.5 so this version allows me to use exactly the same setup as I was using before. If you are starting a new project I would suggest that the 4.6.x series is what you should use as it is substantially faster (for a system I'm running that contains no water on an Intel sandy-bridge system it is more than 50% faster). This series will also probably receive more attention in terms of bug fixes and new releases (though I'm not a developer so I could be wrong about that). Quite right. 4.5.7 is expected to be the last version in the 4.5.x series, and I suspect that will be true unless we discover some catastrophic bug that needs to be patched in older versions. 4.6.x (and the eventual transition to 5.0) will receive the greatest amount of attention from here on out. -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] Doubt about the Gromacs versions
Thanks for your reply. On Thu, Apr 25, 2013 at 7:18 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: The 4.6.1 release is a more advanced version of gromacs with the latest kernels and features (GPU support, verlet cut-offs etc.). 4.5.7 is a maintenance release for those of us who for whatever reason wish to keep using the older 4.5.x series release. It mainly adds fixes made to the 4.6.x series to the 4.5.x version of the code. I use it as most of my calculations were conducted in 4.5.5 so this version allows me to use exactly the same setup as I was using before. If you are starting a new project I would suggest that the 4.6.x series is what you should use as it is substantially faster (for a system I'm running that contains no water on an Intel sandy-bridge system it is more than 50% faster). This series will also probably receive more attention in terms of bug fixes and new releases (though I'm not a developer so I could be wrong about that). Richard On 25/04/13 14:39, bipin singh wrote: Hi, Please let me know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what is the reason behind the update for 4.5.x versions if 4.6.x versions are already available. -- 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] issue in replica exchange
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, state-sd_X, state-natoms);
}
I mis-stated last night - there *is* exchange of ensemble data, but it is
incomplete. In particular, state-ekinstate is not exchanged. Probably it
is incomplete because the 9-year-old comment about t_state changing is in a
location that nobody changing t_state will see. And serializing a complex C
data structure over MPI is tedious at best. But that is not really an
excuse for the non-modularity GROMACS has for many of its key data
structures. We are working on various workflow and actual code structure
improvements to fix/prevent issues like this, but the proliferation of
algorithms that ought to be inter-operable makes the job pretty hard.
Other codes seem to exchange the ensemble label data (e.g. reference
temperatures for T-coupling) because they write trajectories that are
continuous with respect to atomic coordinates. I plan to move REMD in
GROMACS to this approach, because it scales better, but it will not happen
any time soon.
That would explain what I see, but let see what 4.5.7 has to say first.
Great. It may be that there were other issues in 4.5.3 that exacerbated any
REMD problem.
Mark
Tks.
On Apr 25, 2013, at 22:40, Mark Abraham mark.j.abra...@gmail.com wrote:
Thanks for the good report. There have been some known issues about the
timing of coupling stages with respect to various intervals between
GROMACS
events for some algorithms. There are a lot of fixed problems in 4.5.7
that
are not specific to REMD, but I have a few lingering doubts about whether
we should be exchanging (scaled) coupling values along with the
coordinates. (Unlike most REMD implementations, GROMACS swaps the
coordinates, not the ensemble data.) If you can reproduce those kinds of
symptoms in 4.5.7 (whether or not they then crash) then there looks like
there may be a problem with the REMD implementation that is perhaps
evident
only with the kind of large time step Martini takes?
Mark
On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole x.peri...@rug.nl
wrote:
Hi,
I have been recently using the REMD code in gmx-407 and gmx-453 and got
a
few systems crashing for unclear reasons so far. The main tests I made
are
using gmx407 but it is all reproducible with gmx453. The crashing was
also
reproduced (not necessarily at the same time point) on several
architectures.
The system is made of a pair of proteins in a membrane patch and for
which
the relative orientation is controlled by non-native
bond/angles/dihedrals
to perform an umbrella sampling. I use the MARTINI force field but that
might not be relevant here.
The crashes occur following exchanges that do not seem to occur the
correct way and preceded by pressure scaling warnings … indicative of a
strong destabilisation of the system and eventual explosion. Some
information seems to be exchanged inaccurately.
Trying to nail down the problem I got stuck and may be some one can
help.
I placed a pdf file showing plots of bonded/nonbonded energies,
temperatures, box size etc … around an exchange that does not lead to a
crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff
every step with the temperature colour coded as indicated in the first
figure.
From the figure it appears that the step right after the exchange there
is
a huge jump of Potential energy coming from the LJ(SR) part of it.
Although
there are some small discontinuities in the progression of the bond and
angle energy around the exchange they seem to fine. The temperature and
box
size seem to respond to it a few step latter while the
[gmx-users] gmx 4.6.1, Expanded ensemble: weird balancing factors
Dear Gromacs users, I am trying to compute the free energy of hydration of ethane in order to get more familiar with the implementation of expanded ensemble in Gromacs v. 4.6.1. The simulations runs fine and the balancing/weight factors are equilibrated after around 1.6 ns (a short equilibration time but this should be ok for a rough estimate of dG). After this the simulation is continued for another 14 ns. At the end I look at the balancing factors to get a fast estimate of dG and see that they are tiny: MC-lambda information N CoulL VdwLCount G(in kT) dG(in kT) 1 0.000 0.000162900.0 -0.09268 2 0.200 0.00014940 -0.09268 -0.01647 3 0.500 0.00014627 -0.10914 -0.03867 4 1.000 0.00014080 -0.147810.02986 5 1.000 0.20014309 -0.117950.07408 6 1.000 0.40015170 -0.043860.01711 7 1.000 0.60015276 -0.02675 -0.02304 8 1.000 0.80015061 -0.04979 -0.06110 9 1.000 1.00014328 -0.110900.0 When adding these to get dG they value is way off what I get if I use the more traditional approach of separate simulations at each lambda value and using BAR at the end. Does anyone have any ideas why I get these values? Here is my mdp-file: integrator = sd tinit= 0 dt = 0.001 nsteps = 1500 comm-mode = Linear nstcomm = 10 nstlog = 1000 nstenergy= 100 nstlist= 10 ns_type= grid pbc= xyz rlist = 1.0 cutoff-scheme = verlet coulombtype= PME rcoulomb = 1.0 vdw-type = cutoff rvdw = 1.0 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-04 DispCorr= EnerPres tc-grps = System tau_t= 5.0 ref_t = 300 Pcoupl= berendsen tau_p = 10.0 compressibility = 4.5e-5 ref_p= 1.013 gen_vel = no constraints = all-bonds constraint-algorithm = lincs ; Free energy/expanded ensemble free-energy= expanded sc-alpha = 0.5 sc-r-power = 6 init-lambda-state = 0 coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0 calc-lambda-neighbors = 9 nstdhdl = 200 dhdl-print-energy = yes couple-moltype = C1X couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol= no nstexpanded = 100 lmc-stats= wang-landau lmc-move = metropolis lmc-weights-equil = wl-delta weight-equil-wl-delta = 0.001 wl-scale = 0.7 wl-ratio = 0.8 init-wl-delta = 1.0 wl-oneovert = yes Thanks in advance! / Joakim-- 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] xpm2ps issue
Dear Gromacs Users and Developers, I am doing do_dssp analyses using a trajectory and structure file both in pdb format. My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps doesn't show ticks on X-axis. I get following message: Auto-tick spacing failed for X-axis, guessing 10009. Upon do_dssp analyses only on 300 frames, ticks on both Y and X-axis are visible. How can one play around with scales on X-axis? I tried tweaking -bx and -size parameters but didn't help. Any feedback is appreciated. -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -- 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: free energy of system
Dear Justin, Thanks for your response and the perfect tutorial. I found the details I needed in it. Best regards, Sarah -- 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] RMSD from the average structure
Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative structures from your trajectory. Erik On 26 Apr 2013, at 06:59, bipin singh bipinel...@gmail.com wrote: Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can calculate RMSD with respect to whatever structure you like, but the interpretation and justification for doing so are up to you. -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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- *--- 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 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] RMSD from the average structure
Dear Sir, Thanks for the useful insight. On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative structures from your trajectory. Erik On 26 Apr 2013, at 06:59, bipin singh bipinel...@gmail.com wrote: Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can calculate RMSD with respect to whatever structure you like, but the interpretation and justification for doing so are up to you. -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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- *--- 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 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 -- *--- 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] SMD - reproducibility
Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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: Martini with PME, temp two low
Hi Xavier, I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is stable and the energy well conserved (400 ns of run). I do know if it is optimal but it works for my system. Stephane -- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- 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: gmx-users Digest, Vol 108, Issue 165
TL;DR version (longer version below): Due to the stochastic nature of SMD (and pulling experiments in general) it is quite natural that the results for different simulations will not be excatly the same. I would say you are fine. Thing is, if you do ligand unbinding SMD simulations the unbinding process is a stochastic process and the results differ somewhat, most importantly the rupture force (highest force before the rupture event) will differ between the simulations and you'll get a distributions of rupture forces. In a simple two-state model, the slope of force vs time, should be the same for each simulation before and after the rupture event (but probably different slopes before and after the rupture), only the time when the rupture event happens will change. If your system is more complex (say a couple of bonds must be broken before the ligand unbinds), the slope before the rupture may vary between some simulations (in some simulations some of the bonds break earlier than in other simulatons. In http://pubs.acs.org/doi/full/10.1021/jp3115644 i looked into a system which can be described by a two-state model. The results from one typical trajectory are shown, but mostly i discuss the averaged results. If one compares the single trajectory and the averaged, one clearly sees that the trajectories varies around the rupture event, but at the start of the simulations the system behaves almost equal for each simulation. Hope this helps. Greetings Thomas Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org: Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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] RE: Martini with PME, temp two low
nstlist of 2 is a be extreme! Did you try 5! It should be fine … but if your are happy that's ok :)) On Apr 26, 2013, at 12:37 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hi Xavier, I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is stable and the energy well conserved (400 ns of run). I do know if it is optimal but it works for my system. Stephane -- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- 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] xpm2ps issue
On 4/26/13 4:33 AM, Neha Gandhi wrote: Dear Gromacs Users and Developers, I am doing do_dssp analyses using a trajectory and structure file both in pdb format. My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps doesn't show ticks on X-axis. I get following message: Auto-tick spacing failed for X-axis, guessing 10009. Upon do_dssp analyses only on 300 frames, ticks on both Y and X-axis are visible. How can one play around with scales on X-axis? I tried tweaking -bx and -size parameters but didn't help. Any feedback is appreciated. Specify spacing and other matrix properties using an .m2p file passed to the -di flag. -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] Re: SMD - reproducibility
Think i now understand your question. Forget what i wrote before. I could imagine the the 'grompp -t npt.cpt' part is a problem. If the simulations would be numerical reproducible, one should get the same results. As they are not, the results will differ somewhat (would think the more, the longer you simulate). But two different simulations would be more equal to each other, than two simulations which start with different velocity distributions for the particles. If you're interested in an stochastic analysis of your system (meaning simulations which are not equal - performing many pulling experiments in reality, one would also have many different starting points) you could do two things: 1) Run a look npt simulation, and use different frames to start the SMD simulations. From each frame the particles should have a different velocity distribution and the results of the SMD simulations should also differ. (Depending on how many SMD simulations you want to perform, this might get expensive, since the starting frame for SMD should be separated by more then a few ps.) 2) Dump the 'npt.cpt' file and randomly determine new velocities for each particle at the start of each SMD simulation. Since each simulation has a different velocity distribution, the SMD simulation wont be the same. This approach has only one weak point. Due to assigning new random velocities you destroy the thermal equilibrium of the system. But if the system was well equilibrated before, this distrubance should only be small and after the first 100-200 ps of the SMD simulaton the system is in thermal equilibrium. If the complete SMD simulation is much longer (couple of ns), the interesting stuff would happen longer after the inital simulation time with the destroyed equilibrium. Hope this helps Thomas Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org: Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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] Re: SMD - reproducibility
Thanks for this. I think option 2 is more reasonable. However, still do not know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD simulations... On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier schl...@uni-mainz.dewrote: Think i now understand your question. Forget what i wrote before. I could imagine the the 'grompp -t npt.cpt' part is a problem. If the simulations would be numerical reproducible, one should get the same results. As they are not, the results will differ somewhat (would think the more, the longer you simulate). But two different simulations would be more equal to each other, than two simulations which start with different velocity distributions for the particles. If you're interested in an stochastic analysis of your system (meaning simulations which are not equal - performing many pulling experiments in reality, one would also have many different starting points) you could do two things: 1) Run a look npt simulation, and use different frames to start the SMD simulations. From each frame the particles should have a different velocity distribution and the results of the SMD simulations should also differ. (Depending on how many SMD simulations you want to perform, this might get expensive, since the starting frame for SMD should be separated by more then a few ps.) 2) Dump the 'npt.cpt' file and randomly determine new velocities for each particle at the start of each SMD simulation. Since each simulation has a different velocity distribution, the SMD simulation wont be the same. This approach has only one weak point. Due to assigning new random velocities you destroy the thermal equilibrium of the system. But if the system was well equilibrated before, this distrubance should only be small and after the first 100-200 ps of the SMD simulaton the system is in thermal equilibrium. If the complete SMD simulation is much longer (couple of ns), the interesting stuff would happen longer after the inital simulation time with the destroyed equilibrium. Hope this helps Thomas Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org: Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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
[gmx-users] Re: plots in gromacs
hey thanks alot..got it :) - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/plots-in-gromacs-tp5007561p5007694.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
[gmx-users] Re: SMD - reproducibility
Don't know. One idea i have: Take a flexible and a relative rigid system and perform simulations with the same starting conditions (- using -t *.cpt). I would imagine that for the flexible system the trajectories start earlier to deviate, since more stuff could happen (system is more flexible - greater configurational space). For the rigid system the configurational space is smaller, so the probability is higher to always follow the same trajectory if one starts with a predefinded velocity and direction. But don't know if this is true, but it's the first thing which comes to my mind. Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org: Thanks for this. I think option 2 is more reasonable. However, still do not know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD simulations... On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesierschl...@uni-mainz.dewrote: Think i now understand your question. Forget what i wrote before. I could imagine the the 'grompp -t npt.cpt' part is a problem. If the simulations would be numerical reproducible, one should get the same results. As they are not, the results will differ somewhat (would think the more, the longer you simulate). But two different simulations would be more equal to each other, than two simulations which start with different velocity distributions for the particles. If you're interested in an stochastic analysis of your system (meaning simulations which are not equal - performing many pulling experiments in reality, one would also have many different starting points) you could do two things: 1) Run a look npt simulation, and use different frames to start the SMD simulations. From each frame the particles should have a different velocity distribution and the results of the SMD simulations should also differ. (Depending on how many SMD simulations you want to perform, this might get expensive, since the starting frame for SMD should be separated by more then a few ps.) 2) Dump the 'npt.cpt' file and randomly determine new velocities for each particle at the start of each SMD simulation. Since each simulation has a different velocity distribution, the SMD simulation wont be the same. This approach has only one weak point. Due to assigning new random velocities you destroy the thermal equilibrium of the system. But if the system was well equilibrated before, this distrubance should only be small and after the first 100-200 ps of the SMD simulaton the system is in thermal equilibrium. If the complete SMD simulation is much longer (couple of ns), the interesting stuff would happen longer after the inital simulation time with the destroyed equilibrium. Hope this helps Thomas Am 26.04.2013 12:00, schriebgmx-users-requ...@gromacs.org: Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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: Martini with PME, temp two low
Xavier, as i said in my message, this nstlist value is not optimal, but it works !!! if wlll try a higher nstlist value, if I have same problem in futur simulations Thanks again for you help Stephane -- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- 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] Issue with RMSD profile
Hello all, I ran 10ns molecular dynamics simulation of protein ligand complex ..in which protein homology model..finally i analyzed .xtc file which is produced after MD production run..first i plotted RMSD profile of backbone of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it is stabilized in plateau.. My question is fluctuation in RMSD profile from 0.2nm to 0.4 nm is acceptable range or not? Can any body explain this Thank you very much Cheers, Nitin -- 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 with RMSD profile
On 4/26/13 9:33 AM, Sainitin Donakonda wrote: Hello all, I ran 10ns molecular dynamics simulation of protein ligand complex ..in which protein homology model..finally i analyzed .xtc file which is produced after MD production run..first i plotted RMSD profile of backbone of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it is stabilized in plateau.. My question is fluctuation in RMSD profile from 0.2nm to 0.4 nm is acceptable range or not? Can any body explain this That sounds about reasonable for a normal, folded protein of average size, but do realize that a given value of RMSD basically tells you nothing. More detailed assessment of the structure is required. -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] Re: SMD - reproducibility
I am not sure but different force profiles may be due to the non-equilibrium relaxation problem. The path on the energy landscape during the non-equilibrium simulations depends on the pulling rate and/or relaxation of any unknown coordinates correlated with pulling coordinates. If during pulling, correlated coordinates will not be able to relax completely, high energy path is more likely on the energy landscape. Effect of relaxations can be tested by performing simulations at several reduced pulling rate. Also, there are several literature available on the effect of pulling rate during simulations. With best regards, Rajendra On Fri, Apr 26, 2013 at 5:31 PM, Steven Neumann s.neuman...@gmail.comwrote: Thanks for this. I think option 2 is more reasonable. However, still do not know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD simulations... On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Think i now understand your question. Forget what i wrote before. I could imagine the the 'grompp -t npt.cpt' part is a problem. If the simulations would be numerical reproducible, one should get the same results. As they are not, the results will differ somewhat (would think the more, the longer you simulate). But two different simulations would be more equal to each other, than two simulations which start with different velocity distributions for the particles. If you're interested in an stochastic analysis of your system (meaning simulations which are not equal - performing many pulling experiments in reality, one would also have many different starting points) you could do two things: 1) Run a look npt simulation, and use different frames to start the SMD simulations. From each frame the particles should have a different velocity distribution and the results of the SMD simulations should also differ. (Depending on how many SMD simulations you want to perform, this might get expensive, since the starting frame for SMD should be separated by more then a few ps.) 2) Dump the 'npt.cpt' file and randomly determine new velocities for each particle at the start of each SMD simulation. Since each simulation has a different velocity distribution, the SMD simulation wont be the same. This approach has only one weak point. Due to assigning new random velocities you destroy the thermal equilibrium of the system. But if the system was well equilibrated before, this distrubance should only be small and after the first 100-200 ps of the SMD simulaton the system is in thermal equilibrium. If the complete SMD simulation is much longer (couple of ns), the interesting stuff would happen longer after the inital simulation time with the destroyed equilibrium. Hope this helps Thomas Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org: Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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 -- 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
Re: [gmx-users] Re: SMD - reproducibility
there should be an extra option in your mdrun command line if reproducibility is an issue: -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility the value of -reprod is set to no by default, turn on that option and trajectories should be the same. best Andre On Fri, Apr 26, 2013 at 9:25 AM, Steven Neumann s.neuman...@gmail.comwrote: Thanks anyway. I will try tu pull it 20-40 times to tell something. Steven On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Don't know. One idea i have: Take a flexible and a relative rigid system and perform simulations with the same starting conditions (- using -t *.cpt). I would imagine that for the flexible system the trajectories start earlier to deviate, since more stuff could happen (system is more flexible - greater configurational space). For the rigid system the configurational space is smaller, so the probability is higher to always follow the same trajectory if one starts with a predefinded velocity and direction. But don't know if this is true, but it's the first thing which comes to my mind. Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org: Thanks for this. I think option 2 is more reasonable. However, still do not know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD simulations... On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesierschl...@uni-mainz.de ** wrote: Think i now understand your question. Forget what i wrote before. I could imagine the the 'grompp -t npt.cpt' part is a problem. If the simulations would be numerical reproducible, one should get the same results. As they are not, the results will differ somewhat (would think the more, the longer you simulate). But two different simulations would be more equal to each other, than two simulations which start with different velocity distributions for the particles. If you're interested in an stochastic analysis of your system (meaning simulations which are not equal - performing many pulling experiments in reality, one would also have many different starting points) you could do two things: 1) Run a look npt simulation, and use different frames to start the SMD simulations. From each frame the particles should have a different velocity distribution and the results of the SMD simulations should also differ. (Depending on how many SMD simulations you want to perform, this might get expensive, since the starting frame for SMD should be separated by more then a few ps.) 2) Dump the 'npt.cpt' file and randomly determine new velocities for each particle at the start of each SMD simulation. Since each simulation has a different velocity distribution, the SMD simulation wont be the same. This approach has only one weak point. Due to assigning new random velocities you destroy the thermal equilibrium of the system. But if the system was well equilibrated before, this distrubance should only be small and after the first 100-200 ps of the SMD simulaton the system is in thermal equilibrium. If the complete SMD simulation is much longer (couple of ns), the interesting stuff would happen longer after the inital simulation time with the destroyed equilibrium. Hope this helps Thomas Am 26.04.2013 12:00, schriebgmx-users-request@**gromacs.org schriebgmx-users-requ...@gromacs.org : Dear Users, I am running my puling simulations of ligand with constant velocity. First I minimize and equilibrate my system: grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr mdrun -s em.tpr -deffnm em grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr mdrun -s nvt298.tpr -deffnm nvt298 grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p topol.top -o npt298.tpr mdrun -s npt298.tpr -deffnm npt298 Then I run 10 pulling simulations with the same mdp file: grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_1.tpr mpiexec mdrun -s pull_1.tpr -deffnm pull_1 ... grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o pull_10.tpr mpiexec mdrun -s pull_10.tpr -deffnm pull_10 I get 3 different (but similar) profiles (Force vs time) with 10 simulations as some of them produce exactly the same results... In another system with the same methodology I get 10 similar but different profiles. I am wondering why in this case only 3 types are possible... Shall I try grompp without -t npt.cpt ? Steven -- 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
[gmx-users] mdrun on GPU
Hi all, I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4. Can I use the same command line as before for mdrun or other tools? Thank you very much, -- J. -- 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] ATP/Mg+2 parameters
Hello Doe anybody know what is the best (the most suitable) set of parameters to use for ATP/Mg+2 ? I have seen from the literature that people have used mainly either the CHARMM27 parameters or the ones in Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate parameters for use with the AMBER force field. J Comput Chem 24:1016 I would appreciate if you can give me any hints on this. Thanks. 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
Re: [gmx-users] mdrun on GPU
On 4/26/13 10:50 AM, Juliette N. wrote: Hi all, I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4. Can I use the same command line as before for mdrun or other tools? Please read through the documentation here first: http://www.gromacs.org/Documentation/Acceleration_and_parallelization The exact details depend on the configuration of your hardware. -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] Linear Interaction Energy Method (LIE)
Hi, I am trying to calculate ligand binding affinity of Dimeric Protein(198 residues) complexed with a peptide(3 residues) using Linear Interaction Energy method.The water box dimensions of ligand with protein and Ligand in water are considered to be same. I am encountering problem in estimating long range electrostatic interactions for ligand interacting with solvent. I have used PME for coulomb-type (trajectory length is 1ns) The option I used in g_energy to extract long range electrostatic interactions is Coul-Recip and results appear to be strange since,the electrostatic energy(EE for ligand in solvent are more negative than electrostatic for ligand in protein, which implies positive values for delta EE(quite weird!) I just wanted to know what are the proper mdp options in order to get meaningful results and also what is the option in g_energy to get LR interactions, whether usage of Coul-Recip is correct or not? I also want to know the cutoffs to be mentioned in order to calculate SR and LR. Whether I should be using Reaction Field or cut-off for treatment of LR interactions The mdp file which I have been using is attached below title= Protein-Peptide Complex ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 0.5; short-range neighborlist cutoff (in nm) rcoulomb= 0.5; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 pbc= xyz; 3-D PBC DispCorr= EnerPres; account for cut-off vdW scheme gen_vel= no; Velocity generation is off Many thanks in advance for your attention. I'd appreciate any help in this regard. Regards, Hindu Tera -- 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] Re: Manual installation of new analysis tool
Dear Mark Junghans,
I have got it. There is some problem in the Makefile. Thanks for your
suggestions and help
On Fri, Apr 26, 2013 at 11:12 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear Mark Junghans,
Thanks for your valuable suggestions.
I have gone through the README file. It says compatibility with 4.5.x
version. I am using 4.5.5. So, I think its not a problem.
@Junghans: I have installed pkg-config in fact the $ pkg-config --libs
libgmx returns
the expected output; -lgmx -lm
Here I am sending you the README file as attachment. Please go through it.
If needed, I am happy to provide the code also.
Thanks a lot
On Fri, Apr 26, 2013 at 4:21 AM, Christoph Junghans jungh...@votca.orgwrote:
Date: Thu, 25 Apr 2013 22:57:55 +0200
From: Mark Abraham mark.j.abra...@gmail.com
Subject: Re: [gmx-users] Manual installation of new analysis tool
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAMNuMAT=tt7EJxdngFaVCK=
4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy venkat...@gmail.com
wrote:
Dear all,
I have got an analysis tool for analyzing membrane density from
Dr.Luca
monticelli. I have followed the installation instructions as given.
1) First thing is to load GROMACS
$ *source /usr/local/gromacs/bin/GMXRC*
2) Enter the source directory of the program then make
$ cd g_mydensity
$ make
According to the instructions, it should create an executable
*g_mydensity*
but I am getting the following errors
*cc `pkg-config --libs libgmx` g_mydensity.o matrix.o distances.o
Looks like his Makefile is relying on valid pkg-config registration.
I've
no idea for what GROMACS versions under what conditions pkg-config
actually
works, but I suggest you follow his instructions really precisely,
and/or
contact him to resolve any doubtful points.
I added the pkg-config support with version 4.0.7 if I remember correctly.
Without knowing further details, two things come to my mind:
0.) [Trivial] Make sure that pkg-config is actually installed.
1.) Try if
$ pkg-config --libs libgmx
returns some useful output like -lgmx -lm. If not, you might need to
set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does
that for you automatically.
2.) Some functions in libgmx have been renamed/changed in the
development from 4.0 to 4.5 to 4.6, so you might actually need to
change the code, or use the same version as Dr.Luca Monticelli.
Cheers,
Christoph
Mark
dist_mode.o grid_mode.o -o g_mydensity*
*g_mydensity.o: In function `gmx_log2':*
*g_mydensity.c:(.text+0xa8): undefined reference to `log'*
*g_mydensity.o: In function `gmx_invsqrt':*
*g_mydensity.c:(.text+0xf2): undefined reference to
`gmx_invsqrt_exptab'*
*g_mydensity.c:(.text+0x101): undefined reference to
`gmx_invsqrt_fracttab'*
*g_mydensity.o: In function `matrix_convert':*
*g_mydensity.c:(.text+0x381): undefined reference to `cos'*
*g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
*g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
*g_mydensity.c:(.text+0x403): undefined reference to `cos'*
*g_mydensity.c:(.text+0x416): undefined reference to `cos'*
*g_mydensity.c:(.text+0x429): undefined reference to `cos'*
*g_mydensity.c:(.text+0x447): undefined reference to `sin'*
*g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
*g_mydensity.o: In function `get_electrons':*
*g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
*g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
*g_mydensity.o: In function `center_coords':*
*g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
*g_mydensity.o: In function `calc_electron_density':*
*g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'*
*g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'*
*g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'*
*g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'*
*g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'*
*g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'*
*g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'*
[gmx-users] compile error
Dear: I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. Here is my step: ./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc F77=ifort FC=ifort make make install cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-5.0 -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 -DCMAKE_PREFIX_PATH=/opt/intel/mkl/include/fftw -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpiCC -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpicc however, it failed with messages: [ 1%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option ‘-ip’ CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): Error generating /home/albert/install/source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 when I try to run make thank you very much best 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] compile error
You got a warning at configure-time that the nvcc host compiler can't be set because the mpi compiler wrapper are used. Because of this, nvcc is using gcc to compile CPU code whick chokes on the icc flags. You can: - set CUDA_HOST_COMPILER to the mpicc backend, i.e. icc or - let cmake detect MPI and use simply CC=icc CXX=icpc cmake -DGMX_MPI=ON (in this case the normal compiler are used and *if* cmake can detect the MPI libs it will not need the wrappers). Cheers, -- Szilárd On Fri, Apr 26, 2013 at 6:45 PM, Albert mailmd2...@gmail.com wrote: Dear: I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. Here is my step: ./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc F77=ifort FC=ifort make make install cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-5.0 -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 -DCMAKE_PREFIX_PATH=/opt/intel/mkl/include/fftw -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpiCC -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpicc however, it failed with messages: [ 1%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option ‘-ip’ CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): Error generating /home/albert/install/source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 when I try to run make thank you very much best 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] compile error
IC. it works very well now. thanks a lot Albert On 04/26/2013 08:01 PM, Szilárd Páll wrote: You got a warning at configure-time that the nvcc host compiler can't be set because the mpi compiler wrapper are used. Because of this, nvcc is using gcc to compile CPU code whick chokes on the icc flags. You can: - set CUDA_HOST_COMPILER to the mpicc backend, i.e. icc or - let cmake detect MPI and use simply CC=icc CXX=icpc cmake -DGMX_MPI=ON (in this case the normal compiler are used and*if* cmake can detect the MPI libs it will not need the wrappers). 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
[gmx-users] GPU efficiency question
Dear: I've got two GTX690 in a a workstation and I found that when I run the md production with following two command: mpirun -np 4 md_run_mpi or mpirun -np 2 md_run_mpi the efficiency are the same. I notice that gromacs can detect 4 GPU (probably because GTX690 have two core..): 4 GPUs detected on host node4: #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible why the -np 2 and -np 4 are the same efficiency? shouldn't it be faster for -np 4 ? 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] _gpu_id failed
Hello: I am going to run gromacs with command: mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4 but it failed with messages: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364 Fatal error: Expected a string argument for option -gpu_id For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Jede der Scherben spiegelt das Licht (Wir sind Helden) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 4 gcq#330: Jede der Scherben spiegelt das Licht (Wir sind Helden) gcq#330: Jede der Scherben spiegelt das Licht (Wir sind Helden) gcq#330: Jede der Scherben spiegelt das Licht (Wir sind Helden) -- mpirun has exited due to process rank 2 with PID 10440 on node tesla exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). 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] Gromos 54A8 forcefield
Hi All, I just read the paper pertaining to Gromos 54A8. I was wondering if the force field files were available somewhere? Thanks. -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromos-54A8-forcefield-tp5007713.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] _gpu_id failed
On 4/26/13 3:37 PM, Albert wrote: Hello: I am going to run gromacs with command: mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4 but it failed with messages: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364 Fatal error: Expected a string argument for option -gpu_id For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The -gpu_id option needs a continuous string of identifiers (see examples on http://www.gromacs.org/Documentation/Acceleration_and_parallelization). Anything separated by a space is interpreted as a new command-line argument. What you want is -gpu_id 0234 -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] Gromos 54A8 forcefield
On 4/26/13 3:58 PM, Rajat Desikan wrote: Hi All, I just read the paper pertaining to Gromos 54A8. I was wondering if the force field files were available somewhere? ATB is usually a good source for Gromos96 parameter sets: http://compbio.biosci.uq.edu.au/atb/ The latest they have is 54A7, though. -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] How to rescue trr trajectory when two or more corrupted frames exist
If the corrupted frame is at 1000 ps, and you can not get at the data after the corrupted frame by using: trjconv -b 1100 , then I suspect that you don't have any good solution here, unless the developers put in some type of magic number at the start of each frame that you could search for with a c program (perhaps contact the developers of gmx_rescue for advice?) A related question is how you ended up with a long .trr file that has corruption in the middle. Did that corruption happen at runtime or later due to a filesystem problem? If it was a later filesystem problem, then you might look into backup solutions. If it happened at runtime, then it would be useful to figure out what happened because ideally gromacs would not forever append to corrupted files since many of us don't look at information in the .trr files until very late in the analysis and an optional 0.1% loss in efficiency might be reasonable to ensure that this doesn't happen (at least our system admins would tell us so). For that, you'll probably need to provide details, including what version of gromacs you used. Chris. -- original message -- I have some corrupted frames in different trajectories. gmxcheck with .trr trajectories gives extraordinary positions or velocities and with .xtc trajectories gives rise to the magic number error. I am aware of the program gmx_rescue kindly offered to us by its developers. However, this program can only work with .xtc files. It is possible to rescue .trr files when there is a maximum of one corrupted frame by checking the size of healthy frames, chopping the parts of the trajectory before and after, using e.g. programs head and tail with the corresponding integer multiples of one healthy frame in bytes and stitching them together. However, when there is two or more corrupted frames in different locations, although it is not hard to spot the exact locations, it is no longer possible to remove the problematic frames size-wise (or at least it is less likely to succeed than winning the lottery) , since the size of each corrupted frame is non-standard. Is there any corresponding software to gmx_rescue that can be used with .trr files? Is there any other recent program or any other way of coping with the problem? I did not post any details of my systems or the specific error messages I get because I believe my question is clear. Thank you in advance! Best, Yiannis -- 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] Questions about the MFFA boundery implementation of Gromacs?
Dear all: I was using the MFFA version of Gromacs which is provided by m.j.louhivuori at http://md.chem.rug.nl/~mara/mffa.html. I have some quesition about this version: i.I saw the implementation of MFFA always with the flip-flop of lipid.Can I apply the flip-flop with this MFFA version of Gromacs ? ii.I also saw the description of implementation of MFFA along only one direction.Is this available in this MFFA version of Gromacs? Anyone who is familar with it help me. -- 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
