Dear Chris: Thanks for you reply. You are right. The printf in gromacs 4.0.7 is very different from gromacs 4.5.3. and the output file in gromacs 4.5.3 is right. I think they fixed the bug :)
Thank you very much, Kun On Mon, Apr 18, 2011 at 1:41 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Re: energy group exclusions (Justin A. Lemkul) > 2. Re: diverging temperature with pressure coupling (Dommert Florian) > 3. Cylinder Pulling output file pullx.xvg wron > (chris.ne...@utoronto.ca) > 4. Simulation of CNT with Amber forcefield (majid hasan) > 5. Re: Simulation of CNT with Amber forcefield (Justin A. Lemkul) > 6. protein-ligand complex tutorial (ahmet y?ld?r?m) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 18 Apr 2011 07:27:27 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: energy group exclusions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dac201f.2010...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Sikandar Mashayak wrote: > > Also, what about non-bonded interactions within the protein? Does > > exclusion group only exclude the non-bonded interactions between two > > different molecules and non-bonded interactions within the single > > molecule atoms are still computed? > > > > Nonbonded interactions are excluded between each defined pair. Therefore, > with > > energygrp_excl = Protein Protein SOL SOL > > you are excluding all nonbonded interactions between protein atoms (Protein > Protein pair) and between solvent atoms (SOL SOL pair). Protein-solvent > interactions are calculated. The use of energygrp_excl (as documented) > indicates that only nonbonded interactions are affected. That is, bonded > energies should still be calculated for all groups. > > -Justin > > > On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak > > <symasha...@gmail.com <mailto:symasha...@gmail.com>> wrote: > > > > Hi > > > > When we define energy group exclusions e.g. like in manual energygrp > > excl = Protein Protein SOL SOL > > and do md rerun, then only non-bonded interactions between Protein > > and SOL are computed. I am wondering what happens to bonded > > interactions within the protein, do they contribute to energies even > > though we have excluded protein-protein interactions? > > > > thanks > > sikandar > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Mon, 18 Apr 2011 13:41:42 +0200 > From: Dommert Florian <domm...@icp.uni-stuttgart.de> > Subject: Re: [gmx-users] diverging temperature with pressure coupling > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <1303126902.2464.107.camel@fermi> > Content-Type: text/plain; charset="utf-8" > > On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote: > > On 2011-04-18 11.22, Dommert Florian wrote: > > > Hello, > > > > > > oh this nasty ILs ;) I am currently investigating a similar problem, > > > that deals with PR-coupling and my impression is that Leap-Frog is the > > > problem and not PR. Currently I am running simulations with md-vv and > > > MTTK to verify my ideas. On the other hand I am using two tc_groups for > > > my ILs due their difference in size. Unfortunately you have not written > > > which IL you deal with, but thinking about long chain ILs like > > > [BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different > > > molecules differ strongly. Here the big question is why does the > > > barostat influence the thermostat. It seems one has to be very very > > > careful, when choosing the coupling parameter for PR. I did a bunch of > > > simulations just varying the coupling parameter and obtained large > > > differences in the dynamics of my system, while static properties like > > > RDF, density of mass, and pressure look quite fine. For example if I > > > calculate the conductivity including correlation effects the values > > > differ from 2 S/m up to 12 S/m. But so far I also have no idea why ??? > > > I am really happy when I finally got my results with vv and if you are > > > interested I can report back to the list or off-list, just let me know. > > > > > > On the other hand I do not know if the force field could be a problem. > > > PR changes the box size according to a Lagrangian equation of motion in > > > contrast to Berendsen, which just does size rescaling. I do not know > how > > > sensible this equations of motions are in respect to the motion of the > > > atoms. Perhaps one can try to perform simulation with a higher accuracy > > > for the electrostatic interactions. I realized that the standard PME > > > settings are quite poor for ILs. Perhaps the Berendsen pressure > coupling > > > can deal with this, because it forces the box to scale. PR follows its > > > equations of motions and PERHAPS introduces artefacts if the > integration > > > of atomic trajectories is too inaccurate. > > > > > > So my PME settings are like this: > > > > > > rcut=1.3 ( here the force field tells you the number ) > > > pme_order=6 > > > fourierspacing=0.05 > > > rtol=1e-8 > > > > > > This are just approximate values, exact numbers can be calculated by > > > g_pme_error for your system. > > > > > Florian, these PME values are scary! Are you running in double precision > > too, otherwise I guess it will be difficult to get the errors as low as > > you want them. > > Hello David, > > these settings yield an accuracy of 10^-4 kJ/(mol nm), which should be > captured by a single precision calculation, if I take into account that > I have forces around 100kJ/(mol nm). Am I wrong ? > > > As regards the Temperature diversion (no pun intended), this is a known > > issue also with Berendsen T,P coupling. The reason for this is lack of > > interaction between the different subsystems. It is interesting to hear > > the PR makes it worse though, because of the better ensemble properties. > > > > If this also has an effect on dynamic properties all of us are in even > > more trouble. I recently had problems reproducing dielectric constants. > > I will now redo my simulation with Berendsen P-coupling instead of PR, > > even though grompp tells me not to! > > > > So I assume the rerun with Berendsen will give you faster dynamics, > which I had when using Berendsen. However as you mentioned you get into > problems for creating a correct canonical ensemble. > > Cheers, > > Flo > > > > > Cheers, > > > > > > Flo > > > > > > > > > On Sun, 2011-04-17 at 03:10 -0400, Roland Schulz wrote: > > >> Forwarding this email from my group colleague: > > >> > > >> > > >> Dear Gromacs users, > > >> > > >> > > >> > > >> I am trying to simulate a cellulose fiber in an ionic liquid solution > > >> in the NPT ensemble. During the simulation, the entire system is > > >> coupled to a thermostat. Yet, I observe an inhomogeneous temperature > > >> distribution throughout my system (hot-solvent/cold-solute) when I use > > >> Parrinello-Rahman pressure coupling but NOT when I employ Berendsen > > >> pressure coupling. I have tested velocity-rescaling and the > > >> Nose-Hoover scheme to keep the temperature constant and in both cases > > >> Parrinello-Rahman pressure coupling seems to cause the solute’s > > >> temperature to become significantly lower than the solvent’s (to > > >> decompose temperatures, I am using “mdrun -rerun” with a run input > > >> that defines tc_grps separately). > > >> > > >> > > >> > > >> I was wondering whether there were any known algorithmic reasons for > > >> this unphysical temperature gradient when using Parrinello-Rahman > > >> pressure coupling. > > >> > > >> Thank you. > > >> > > >> Barmak > > >> > > >> > > >> Comment from me: The effect is large. The ionic liquid is 5 degrees > > >> higher and the cellulose is 50 degrees lower (after 50ps, after that > > >> it stays constant). With Berendsen pressure both parts fluctuate > > >> around the same target temperature (as one would expect). Any reason > > >> why one doesn't get the correct temperature with rerun? Or is their a > > >> better way to get the temperature for different groups(for a > > >> simulation with just one tc-group)? Any reason why Parrinello-Rahman > > >> pressure coupling would have this effect on the temperature? > > >> > > >> > > >> Roland > > >> > > >> > > >> -- > > >> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > > >> 865-241-1537, ORNL PO BOX 2008 MS6309 > > >> -- > > >> gmx-users mailing list gmx-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 > > > > > > > > > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > -- > Florian Dommert > Dipl. - Phys. > > Institute for Computational Physics > University Stuttgart > > Pfaffenwaldring 27 > 70569 Stuttgart > > EMail: domm...@icp.uni-stuttgart.de > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > Tel.: +49 - (0)711 - 68563613 > Fax.: +49 - (0)711 - 68563658 > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/pgp-signature > Size: 198 bytes > Desc: This is a digitally signed message part > Url : > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110418/8c5b089d/attachment-0001.bin > > ------------------------------ > > Message: 3 > Date: Mon, 18 Apr 2011 11:53:28 -0400 > From: chris.ne...@utoronto.ca > Subject: [gmx-users] Cylinder Pulling output file pullx.xvg wron > To: gmx-users@gromacs.org > Message-ID: <20110418115328.1gv8f4f0asg04...@webmail.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > That part of the pull code has a different printf statement in version > 4.5.3. Can you test 4.0.7 output vs. 4.5.3 output and see if 4.5.3 is > correct? You could simple use nsteps=0 genvel=no and load a .gro with > no velocities in your mdrun. > > Chris. > > -- original message -- > > I am trying cylinder pulling as an option of umbrella sampling using > gromacs > 4.0.7. Things seem to work but I noticed that in the output file pullx.xvg, > the referece group's postion is always 0. I don't think it is right. When I > use position pulling, the reference position is never 0. > > Thanks for you help. > Kun > > Below is my .mdp file > pull = umbrella > pull_geometry = cylinder > pull_r1 = 1.0 > Pull_r0 = 1.0 > pull_dim = N N Y > pull_start = yes > pull_init1 = 0.0 > pull_ngroups = 1 > pull_group0 = group0 > pull_group1 = group1 > pull_rate1 = 0.01 > pull_vec1 = 0.0 0.0 -1.0 > pull_k1 = 3000 ; kJ mol^-1 nm^-2 > pull_nstxout = 1000 > pull_nstfout = 1000 > > Here is the output: > > @ title "Pull COM" > @ xaxis label "Time (ps)" > @ yaxis label "Position (nm)" > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend "0 Z" > @ s1 legend "1 dZ" > 0.0000 0 5.69818 > 2.0000 0 5.67685 > 4.0000 0 5.68564 > 6.0000 0 5.65461 > 8.0000 0 5.63482 > 10.0000 0 5.61658 > 12.0000 0 5.61679 > 14.0000 0 5.54434 > 16.0000 0 5.55352 > 18.0000 0 5.4964 > -------------- next part ------------- > > > > ------------------------------ > > Message: 4 > Date: Mon, 18 Apr 2011 10:17:12 -0700 (PDT) > From: majid hasan <pu_majidha...@yahoo.com> > Subject: [gmx-users] Simulation of CNT with Amber forcefield > To: gms-users mailing list <gmx-users@gromacs.org> > Message-ID: <674190.93212...@web38304.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear All, > > I am doing a DNA-CNT simulation, and I am trying to generate a topology of > CNT > using Amber99, which has been used for such systems, and CNT atoms are > modeled > using sp2 carbon parameters. > > But when I try to create topology file using: pdb2gmx -f cnt.pdb -p > cnt.top, and > Amber99 forcefield, I get this error: > Fatal Error: > Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while > sorting > atoms. > > During the execution, it says "There are 1 chains and 0 blocks of water and > 1 > residues with 168 atoms" after analyzing pdb file. > > So I suspect problem is that it reads carbon as a residue in my .pdb file. > > If this is the problem, then how do I make sure that it reads carbon as an > atom > and not a residue? > > My .pdb file has entries of the form: > ATOM 1 C C A 1 4.039 .... > ATOM 2 C C A 1 3.97 .... > > Thanks for your help, > Majid > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110418/ee4b8cd9/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 18 Apr 2011 13:25:39 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dac7413.9090...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > majid hasan wrote: > > Dear All, > > > > I am doing a DNA-CNT simulation, and I am trying to generate a topology > > of CNT using Amber99, which has been used for such systems, and CNT > > atoms are modeled using sp2 carbon parameters. > > > > But when I try to create topology file using: pdb2gmx -f cnt.pdb -p > > cnt.top, and Amber99 forcefield, I get this error: > > Have you created an .rtp entry for your CNT? I doubt that it's even > possible > for cyclic molecules like this one. pdb2gmx is only useful for linear > molecules > composed of repeating building blocks, with limited support for branching. > You > may want to consult: > > http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube > > Some of that information is outdated, but there is a plethora of > information in > the list archive about proper CNT topology generation. Search for posts by > Christopher Stiles. > > > Fatal Error: > > Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while > > sorting atoms. > > > > This answers my question above. Your structure is being interpreted as > RNA. > Without significant effort and perhaps code modification, pdb2gmx is not > likely > to be useful here. > > > During the execution, it says "There are 1 chains and 0 blocks of water > > and 1 residues with 168 atoms" after analyzing pdb file. > > > > So I suspect problem is that it reads carbon as a residue in my .pdb > file. > > > > If this is the problem, then how do I make sure that it reads carbon as > > an atom and not a residue? > > > > My .pdb file has entries of the form: > > ATOM 1 C C A 1 4.039 .... > > ATOM 2 C C A 1 3.97 .... > > > > Well, you've named your residues "C" and the component atoms "C" so there's > no > real confusion about anything. It's also not the source of your problems. > > g_x2top may be a useful program for generating a topology, or perhaps other > software that is entirely unrelated to Gromacs. > > -Justin > > > Thanks for your help, > > Majid > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Mon, 18 Apr 2011 20:40:49 +0300 > From: ahmet y?ld?r?m <ahmedo...@gmail.com> > Subject: [gmx-users] protein-ligand complex tutorial > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTi=qgpp3bc+egscomvruvr7acfw...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Justin, > > You prepared a useful tutorial. if you used PO4 ligand (which has 2 > molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and .gro > files of ligand because of 2 molecule, what change? > Can you give some hint? > Thanks > > 3HTB.pdb > .... > > TER 1365 ASN A 163 > HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P > HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O > HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O > HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O > HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O > HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P > HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O > HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O > HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O > HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O > HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C > .. > > > > -- > Ahmet YILDIRIM > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110418/079893ae/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-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! > > End of gmx-users Digest, Vol 84, Issue 150 > ****************************************** > -- Kun Huang Department of Physics, Rensselaer Polytechnic Institute. Troy, NY. 12180.
-- gmx-users mailing list gmx-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