Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
Hi Berk, thanks for the trick. Unfortunately I'm not in my lab right now and can't open easily xterms over the network. I'll try to catch up once I'm back (end of December), unless Bernhard or Antoine find the solution. Cheers, Patrick Berk Hess a écrit : Hi, You can do something like: mpirun -np 4 xterm -e gdb ~/check_gmx/obj/g_x86_64/src/kernel/mdrun with the appropriate settings for your system. You will have to type run in every xterm to make mdrun run. Or you can make some scripts (gdb -x gdb_cmds will read the gdb commands from the file gdb_cmds). When you think it hangs, type ctrl-c in an xterm and type where to see where it hangs. I would guess this would be in an MPI call. Berk Date: Mon, 15 Dec 2008 23:53:45 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi Berk, I used gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC). I recompiled it with CFLAGS=-g and it still hangs... Now, how can we run it in the debugger ? Thanks, Patrick Berk Hess a écrit : Hi, What compiler (and compiler version) are you using? Could you configure with CFLAGS=-g and see if it still hangs? If it also hangs in that case, we can run it in the debugger and find out where it hangs. Berk Date: Mon, 15 Dec 2008 16:32:31 +0100 From: patrick.fu...@univ-paris-diderot.fr To: gmx-users@gromacs.org Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Hi, I have exactly the same problem under Fedora 9 on a dual-quadricore (Intel Xeon E5430, 2.66 GHz) computer. Gromacs-4.0.2 is hanging (same for gromacs-4.0.0) after a couple of minutes of simulation. Sometimes, it even hangs very quickly before the simulation reaches the writing of the first checkpoint file (in fact the time length before the hang occurs is chaotic, sometimes a couple of minutes, or a few seconds). The CPUs are still loaded but nothing goes to the output (on any file log, xtc, trr, edr...). All gromacs binaries were standardly compiled with --enable-mpi and the latest lam-7.1.4. As Bernhard and Antoine I don't see anything strange in the log file. I have another computer single quadricore (Intel Xeon E5430, 2.66 GHz) under Fedora 8 and the same system (same mdp, topology etc...) is running fine with gromacs-4.0.2 (compiled with lam-7.1.4 as well). So would it be possible that there's something wrong going on with FC9 and lam-7.1.4...? Cheers, Patrick Berk Hess a écrit : Hi, If your simulations no longer produce output, but still run and there is no error or warning message, my guess would be that they are waiting for MPI communication. But the developers any many users are using 4.0 and I have not heard from problems like this, so I wonder if the problem could be somewhere else. Could you (or have your tried to) continue your simulation from the last checkpoint (mdrun option -cpi) before the hang, to see if it crashes quickly then? Berk Date: Fri, 12 Dec 2008 13:42:43 +0100 From: bernhard.kn...@meduniwien.ac.at To: gmx-users@gromacs.org Subject: Subject: Re: Re: [gmx-users] Gromacs 4 bug? Mark wrote: What's happening in the log files? What's the latest information in the checkpoint files? Could there be some issue with file system availability? Hi Mark Unfortunaltey I already deleted the simulation files which got stuck after 847ps. But here is the output of another simulation done on the same system but with an other pdb file. This one gets stuck after 179ps with the following output: The latest thing the checkpoint file says is: imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009 imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009 The predcition for 1st of July is not surprising since I am always parameterizing the simulation with 200ns to avoid to restart it if something interesting happens in the last frames. for the .log file it is: Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04 LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05 DD step 88999 load imb.: force 3.1% Step Time Lambda 89000 178.2 0.0 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 8.03089e+03 3.59681e+03
Re: [gmx-users] Free energy of transfer with accuracy
Chris, Also, if your C60 is hollow, I can imagine that it might exclude solvent atoms from the inside, in which case you are going to have a big convergence issue as solvent begins to interpenetrate with the C60, which may lead to noise problems when this starts to happen, whatever soft core functional form you use. This just means you will need to run longer simulations in this regime. Which makes sense. Do you know a reference for this phenomenon? Er, no. You can reference a personal communication from me saying that my data suggests this is likely. :) Personal experience tells me that this would probably be the case but I haven't ever seen a publication on this. David David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA 70148 dlmob...@uno.edu Office 504-280-6445 Fax 504-280-6860 Thanks, Chris. -- original message -- Eudes, On Thu, Dec 11, 2008 at 8:27 AM, Eudes Fileti fil...@ufabc.edu.br wrote: [Hide Quoted Text] Hello David, thanks for the reply! I am simulating the free energy of transfer of the C60, from ethanol to benzene. The softcore parameters, I used the are the same values of Tieleman et.al. (nature nanotechnology, 3, 363). At figure, each curve refers to a different solvent; one of them for ethanol and another for benzene. For lambda=0 I have the Coulomb and LJ parameters turn on and for lambda=1, turn off. I have found a large difference when simulating my system using sc_power=2. See in this link ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg ) the comparison between plots from sc_power=1 and sc_power=2 for solute in benzene. Near 0 and 1, I believe that problem cancels out at difference, as can seen at ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ) . Then the main problem, in my view, is in the intermediate region, where the plot presents a deep (-500 units) and noise minimum. Observe that in lambda=0, sc_power=2 reduce largely the derivative, but the critical region, one that makes the difference in calculation of the transfer free energy, remains the same, ie, the derivative still oscilates a lot and is not smooth. Are you believe that changing the value of alpha from 0.47 to 0.50 can resolve this? OK, there are several issues here. 1) The noisy minimum in dV/dlambda 2) The overall shape of dV/dlambda 3) Other potential problems On (1), the noisiness of the minimum you refer to really means there are convergence problems for some reason -- probably correlation times are particularly long there. This may be helped by using the soft core parameters I mention, but I am not sure. See item #3. On (2), in general, the overall shape of dV/dlambda seems to be smoothest and best behaved with the particular soft core parameters I mention. We did a lot of testing on this (i.e., many values of alpha at each of several sc-power values). On (3), there are other thing that can go wrong when using soft core. See http://www.alchemistry.org/wiki/index.php/Best_Practices for some discussion, and see rule #2 in particular. If you have any partial charges on atoms in your C60 this could be a potential source of error and noise. Also, if your C60 is hollow, I can imagine that it might exclude solvent atoms from the inside, in which case you are going to have a big convergence issue as solvent begins to interpenetrate with the C60, which may lead to noise problems when this starts to happen, whatever soft core functional form you use. This just means you will need to run longer simulations in this regime. Anyway, long story short, I suggest two things: (a) Make sure you turn off partial charges on C60 (without using soft core) before turning off the LJ using soft core, and (b) use the soft core functional form I suggest. David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Free energy of transfer with accuracy
Eudes, But first I would want to know two things. 1) The parameter sc-sigma of 0.5 is reasonable? How this parameter affects the shape of dvdl plot? You performed tests about it? I found little about it in the forum. Check out the manual on what this parameter does. IIRC it only applies to atoms which have sigma parameters of zero to begin with (i.e. hydrogens) and so it really doesn't do much. 2) In my tests, I realized that, simply changing the electrostatic interactions treatment (cut-off or PME), a large difference it was found at hydration free energy. Of course. Long-range interactions make big differences in this sort of thing. You should be using lattice-sum (i.e. PME) electrostatics if you care about accuracy. With cutoff I have found 12.2kJ/mol while with PME, 24.0kJ/mol. The accepted value must be around 20kJ/mol). This to me was somewhat surprising, because, as mentioned above, C60 does not have charge, so that effect should be minimized or zero. In any case I assign it to the electrostatic of the solvent. I suppose the PME result is more reliable, it's ok? Do you know some work that explore the effect of the electrostatic of the solvent on the solvation free energy? Treatment of long range electrostatics effects the solvent generally, including the effective hydrogen bond strength and structure, solvent density, etc. So it's not that surprising it should affect the hydration free energy. Also, if you think about it, a hypothetical water molecule at the center of a C60 will have very different interactions with its environment depend on whether or not it sees water far away. I would think it would cost more to create a cavity with PME than without PME because of this effect, which I think is consistent with the numbers you're giving (though you didn't specify your sign convention). The other thing that actually could affect this significantly is treatment of long-range dispersion interactions. I have a separate publication with Michael SHirts on that if you are interested (see http://www.dillgroup.ucsf.edu/~dmobley). In terms of effects of electrostatics on solvation free energy, I am not sure whether anyone has studied this explicitly, but certainly the effects of electrostatics on water structure generally are well known and studied. David Thank you eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: bc2c99750812110724tc388a77p1577e9c999a6d...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Eudes, On Thu, Dec 11, 2008 at 8:27 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Hello David, thanks for the reply! I am simulating the free energy of transfer of the C60, from ethanol to benzene. The softcore parameters, I used the are the same values of Tieleman et.al. (nature nanotechnology, 3, 363). At figure, each curve refers to a different solvent; one of them for ethanol and another for benzene. For lambda=0 I have the Coulomb and LJ parameters turn on and for lambda=1, turn off. I have found a large difference when simulating my system using sc_power=2. See in this link ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-scpower.jpg ) the comparison between plots from sc_power=1 and sc_power=2 for solute in benzene. Near 0 and 1, I believe that problem cancels out at difference, as can seen at ( http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ) . Then the main problem, in my view, is in the intermediate region, where the plot presents a deep (-500 units) and noise minimum. Observe that in lambda=0, sc_power=2 reduce largely the derivative, but the critical region, one that makes the difference in calculation of the transfer free energy, remains the same, ie, the derivative still oscilates a lot and is not smooth. Are you believe that changing the value of alpha from 0.47 to 0.50 can resolve this? OK, there are several issues here. 1) The noisy minimum in dV/dlambda 2) The overall shape of dV/dlambda 3) Other potential problems On (1), the noisiness of the minimum you refer to really means there are convergence problems for some reason -- probably correlation times are particularly long there. This may be helped by using the soft core parameters I mention, but I am not sure. See item #3. On (2), in general, the overall shape of dV/dlambda seems to be smoothest and best behaved with the particular soft core parameters I mention. We did a lot of testing on this (i.e., many values of alpha at each of several sc-power values). On (3), there are other thing that can go wrong when using soft
[gmx-users] What water topology is worth using?
Hello, what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? Thanks SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] What water topology is worth using?
On Wed, 17 Dec 2008 20:55:28 +0300 DimitryASuplatov gene...@gmail.com wrote: Hello, what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? Don't worry this comment was probably based on personal/dogmatic believe and not on actual data. TIP3p and SPC are pretty much of same quality. SPC/E is probably better though. Thanks SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Gromacs 4 with mpi interface
Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. And after adding some ions using genion when i try to run grompp again before final mdrun i get some error telling mismatches in .top and .gro file in some atoms although i have changed the top files as normally we should adding the ions and changing the total number of solvents accordingly..Why is it happening Can anybody help..plzz?? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
Chitrita Dutta Roy wrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. Installation instructions are on the Gromacs webpage and the wiki site (including a heading called Using MPI). And after adding some ions using genion when i try to run grompp again before final mdrun i get some error telling mismatches in .top and .gro file in some atoms although i have changed the top files as normally we should adding the ions and changing the total number of solvents accordingly..Why is it happening Can anybody help..plzz?? Then you haven't updated your topology correctly. Without seeing your command line and the output, it's hard to say much more. The wiki site (again) is your friend here. -Justin Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
What exactly Do we need to change in the topology file suppose if we add 2 NA+ ions in the system..??? On Thu, Dec 18, 2008 at 1:45 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. Installation instructions are on the Gromacs webpage and the wiki site (including a heading called Using MPI). And after adding some ions using genion when i try to run grompp again before final mdrun i get some error telling mismatches in .top and .gro file in some atoms although i have changed the top files as normally we should adding the ions and changing the total number of solvents accordingly..Why is it happening Can anybody help..plzz?? Then you haven't updated your topology correctly. Without seeing your command line and the output, it's hard to say much more. The wiki site (again) is your friend here. -Justin Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
From genion -h: genion replaces solvent molecules by monoatomic ions at the position of the first atoms with the most favorable electrostatic potential or at random. That would explain how genion works, and what you must do to update the topology correctly. If you have added 2 NA+, then you have also removed 2 SOL. -Justin Chitrita Dutta Roy wrote: What exactly Do we need to change in the topology file suppose if we add 2 NA+ ions in the system..??? On Thu, Dec 18, 2008 at 1:45 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. Installation instructions are on the Gromacs webpage and the wiki site (including a heading called Using MPI). And after adding some ions using genion when i try to run grompp again before final mdrun i get some error telling mismatches in .top and .gro file in some atoms although i have changed the top files as normally we should adding the ions and changing the total number of solvents accordingly..Why is it happening Can anybody help..plzz?? Then you haven't updated your topology correctly. Without seeing your command line and the output, it's hard to say much more. The wiki site (again) is your friend here. -Justin Thanks. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] RE: What water topology is worth using?
what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? I think it much depends on what exact properties you calculate. You may calculate something very specific... I can suggest you a lot of water models but I'm sure none of them is much better than another ones. I don't consider that tip3p is the best one. Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] RE: Gromacs 4 with mpi interface
Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. The most primitive way would be probably ./configure --enable-mpi make make install For more info please find and read the INSTALL file in the gromacs installation folder. Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] What water topology is worth using?
Thank you for answering. One more question. As I learned spc is for use with GROMOS and tip3p - with OPLS AA. I use OPLS AA. Should I consider using tip3p or it does not really matter? Thank you. On Wed, 2008-12-17 at 19:41 +0100, Xavier Periole wrote: On Wed, 17 Dec 2008 20:55:28 +0300 DimitryASuplatov gene...@gmail.com wrote: Hello, what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? Don't worry this comment was probably based on personal/dogmatic believe and not on actual data. TIP3p and SPC are pretty much of same quality. SPC/E is probably better though. Thanks SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php - XAvier Periole - PhD - Molecular Dynamics Group - Computation and NMR University of Groningen The Netherlands - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re[2]: What water topology is worth using?
Hi Dimitry, D field I`m using. Can I use spc with OPLS AA? I think you can. As for me when simulating water I prefer SPC/E but it's only my personal taste. Best, Vitaly D Thank you for answering. D Nevertheless I believe that each model is based on appropriate force D field. As I learned tip3p is based on OPLS AA and this is exactly the D field I`m using. Can I use spc with OPLS AA? D Thank you D On Wed, 2008-12-17 at 22:49 +0200, Vitaly Chaban wrote: what solvent topology do you use in your simulations? I`ve always used spc and had no problems with it. Though recently I`ve heard that tip3p is better. What do you suggest? What do you use? I think it much depends on what exact properties you calculate. You may calculate something very specific... I can suggest you a lot of water models but I'm sure none of them is much better than another ones. I don't consider that tip3p is the best one. Vitaly === Vitaly V. Chaban, Ph.D.-student School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
U just have to modify the .top file, Just add the line Na+ 2 at the bottom of the file where u can find SOL some numberand also u have to substract 2 from the SOL number. Thats it. Regarding MPI, if u r using MULTIPLE MACHINESthen MPI is useful otherwise , if u r using single machine with multiple processors,run the command mdrun -np no.of processors -s topol -v -N no.of processors That's it.Regarding the installation of MPI, first u should install the all library files that are mentioned in the Gromacs web site, lam-7.0.6-5.x86_64.rpm,libaio-0.3.103-3.x86_64.rpm,libaio-devel-0.3.103-3.x86_64.rpm and fftw . On Thu, Dec 18, 2008 at 1:03 AM, Chitrita Dutta Roy chitrita...@gmail.comwrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. And after adding some ions using genion when i try to run grompp again before final mdrun i get some error telling mismatches in .top and .gro file in some atoms although i have changed the top files as normally we should adding the ions and changing the total number of solvents accordingly..Why is it happening Can anybody help..plzz?? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
Hi, Please don't top post, particularly when responding to multiple topics in one email, as it makes it hard for people to understand the context of your remarks. A better approach is to insert new paragraphs after the text you refer to. You can also appear to be a more credible source of good advice by spelling you and are correctly, and avoiding ALL CAPITALS. Abbreviations are good for casual or bandwidth-limited situations, which don't really apply here. :-) Here's a good link on how to ask and answer questions well :-) http://www.catb.org/~esr/faqs/smart-questions.html U just have to modify the .top file, Just add the line Na+ 2 at the bottom of the file where u can find SOL some numberand also u have to substract 2 from the SOL number. Thats it. Regarding MPI, if u r using MULTIPLE MACHINESthen MPI is useful otherwise , if u r using single machine with multiple processors,run the command mdrun -np no.of processors -s topol -v -N no.of processors MPI is needed for any form of parallelism with GROMACS. That's it.Regarding the installation of MPI, first u should install the all library files that are mentioned in the Gromacs web site, lam-7.0.6-5.x86_64.rpm,libaio-0.3.103-3.x86_64.rpm,libaio-devel-0.3.103-3.x86_64.rpm and fftw . Rather than copying and pasting information, a link like http://www.gromacs.org/content/view/23/33/ is usually more appropriate. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Gromacs 4 with mpi interface
On Thu, 2008-12-18 at 01:03 +0530, Chitrita Dutta Roy wrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. Just install using yum: # yum -y install gromacs gromacs-mpi Due to some clashing names, all binaries have been renamed to start with g_, i.e. mdrun is g_mdrun and so on. Everything is compiled both in single and double precision, and MPI binaries are available of mdrun (and once the Makefiles are updated I'll put in also the MPI enabled analysis tools). Example: g_mdrun single precision g_mdrun_d double precision g_mdrun_mpi single precision MPI g_mdrun_mpi_d double precision MPI -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
