[gmx-users] Re: Re: Re: Re: Simulation of silicon oxide surfaces
David van der Spoel spoel at xray.bmc.uu.se wrote: [reference to articles] Thanks for the reference to your article and that of Wensink, that looks exactly like the information I need... Best regards, Michael Hirtz -- http://www.defux.de ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] new version of C terminus database for charmm
Hi, I am trying to run gromacs with charmm forcefield. # I had run the perl program convert_charmm_to_gromacs.pl and put the output files ffcharmmbon.itp and ffcharmmnb.itp into the gromacs share/gromacs/top directory. # I had put all the files from the tar file into the share/gromacs/top directory. # I had updated the FF.dat file to include the charmm file. # I undersatand that the format of the termini database have changed for the 3.3.2 version. I could make the changes in ffcharmm-n.tdb. Accordingly I tried to make the changes in ffcharmm-c.tdb, but when I give the command pdb2gmx -f 1aoc.gro -ff charmm -ter I get the following error Reading Termini Database: expected 3 items of atom data in stead of 1 on line O OC 15.9994 -0.670 I guess the ffcharmm-c.tdb file has not been changed correctly.Has anyone done it? I will be grateful if someone can help me in this. Thanks in advance Sarbani___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: a tip to run gromacs from Fink in mac duo core
Thanks vdSpoel, Just one more question. So, in a dual/quad core computer, do -sort -shuffle do any difference for better? I mean, is there use for 'sort and shuffle' in a multi-core computer (not cluster!)? Cheers, Alan On Tue, Jul 22, 2008 at 4:26 PM, Alan [EMAIL PROTECTED] wrote: Hi list! I would like to know among mac intel users with Fink, which gromacs with mpi to use: gromacs-mpi-lammpi or gromacs-mpi-openmpi Or there's any easier way (multi-threads is still not working in GMX, right?)? Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: a tip to run gromacs from Fink in mac duo core
Alan wrote: Thanks vdSpoel, Just one more question. So, in a dual/quad core computer, do -sort -shuffle do any difference for better? I mean, is there use for 'sort and shuffle' in a multi-core computer (not cluster!)? Definitely, because shuffle will enhance the load balancing (unless you have just one protein in water) and sort the locality of the data. This will enhance the performance on both shared and distributed memory. Cheers, Carsten Cheers, Alan On Tue, Jul 22, 2008 at 4:26 PM, Alan [EMAIL PROTECTED] wrote: Hi list! I would like to know among mac intel users with Fink, which gromacs with mpi to use: gromacs-mpi-lammpi or gromacs-mpi-openmpi Or there's any easier way (multi-threads is still not working in GMX, right?)? Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to build boxes with constant number of solvent molecules?
Hello dears, I want to solvate different conformations of a molecule in a water box and I want to have the same number of solvent molecules in my box at the end. I do it with genbox but end up with different number of solvent molecules. A random insertion of more molecules results in a box which would not be easily equilibrated. I also tried to solvate in a larger box and then delete some molecules from the end of file so that I have a certain number of molecules for all of them, but it also results in a strange looking environments in the box which mostly lead to an equilibration crash. Does one know any practical strategy to solvate a molecule in a box and have the number of solvent molecules fixed?? I appreciate any suggestions, regards, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topologies from autodock
hi, I have got a docked complex (ligand and protein) in pdb format from autodock. I am unable to generate topoloy file for the docked complex, (but, I can do the same for protein and ligand separately). Can any of you please guide me in generating topoloy file for the docked complex.. Let me be more candid, I am novice in this field.regards,Kaushik From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genion strips +, -, digits. Bug or feature?
Dear all I have added the new AMBER ion definitions from Joung and Cheatham to my ffamber* force field files. Following the nomenclature these ions have in AMBER, I use the same name for the atom name, the residue name, and the molecule type, which includes the charge. E.g., I have In ions.itp: [ moleculetype ] K+ 3 [ atoms ] 1 amber99_92 1 K+ K+1 1 39.1 and correspondingly In ffamber*nb.itp: amber99_92 K+ 0. 0. A 3.03796E-01 8.10369E-01 Now, when using genion -pname K+ (or -pname K+ or -pname 'K+') I get ion entries in the gro file for K+ residues containing K atoms, rather than K+ atoms. Naively, I had assumed that the name defined with -pname is the residue name (= molecule type) and that genion looks up the corresponding atom name in ions.itp. This is obviously not the case... Some playing around seems to suggest that the string supplied with - pname is indeed used as the residue name. However, +, -, and any preceding or following digits are then stripped to produce the atom name. So, e.g., -pname Xyz3% gives Xyz3% for both residue and atom names, whereas -pname Xyz-3 produces atoms named Xyz. Is this an undocumented (and rather annoying and unnecessary) feature or a bug? Cheers Hans ... Dr. Hans Martin Senn Lord Kelvin/Adam Smith Research Fellow E-mail: [EMAIL PROTECTED] Direct line: +44 (0)141 330 6574 Fax: +44 (0)141 330 4888 Department of Chemistry Joseph Black Building University of Glasgow Glasgow G12 8QQ Scotland, UK ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Is it correct
Dear justin In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please say me Is that correct. title = cpeptide MD cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 5 ps. nstcomm = 1 nstxout = 50 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein sol ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 -- 2)In the place program doesent have phrase for example PME,does. the gromacs use default? 3)when I use berendsen coupling is on and pcoup =yes and In my work is effect in fluctuate? best sh-karbalaee ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] new version of C terminus database for charmm
sarbani chattopadhyay wrote: Hi, I am trying to run gromacs with charmm forcefield. # I had run the perl program convert_charmm_to_gromacs.pl and put the output files ffcharmmbon.itp and ffcharmmnb.itp into the gromacs share/gromacs/top directory. # I had put all the files from the tar file into the share/gromacs/top directory. # I had updated the FF.dat file to include the charmm file. # I undersatand that the format of the termini database have changed for the 3.3.2 version. I could make the changes in ffcharmm-n.tdb. Accordingly I tried to make the changes in ffcharmm-c.tdb, but when I give the command pdb2gmx -f 1aoc.gro -ff charmm -ter I get the following error Reading Termini Database: expected 3 items of atom data in stead of 1 on line O OC15.9994 -0.670 I guess the ffcharmm-c.tdb file has not been changed correctly.Has anyone done it? I will be grateful if someone can help me in this. This was a strange error; I remember coming across it as well. No modification that I could make to that line alleviated the problem, and I still don't know why. What I ended up doing was changing the [ COO- ] section to the following: [ COO- ] [ replace ] C CC 12.0110 0.340 [ add ] 2 8 O C CA N OC 15.999 -0.670 [ delete ] O [ impropers ] C CA O2 O1 improper_OB_X_X_CD_ Therefore, instead of replacing O by OC, the O is deleted, and an OC added back in its place. I don't know why that works, and the replace function doesn't, so maybe someone else has a better idea, but this is how I got around it. -Justin Thanks in advance Sarbani Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is it correct
shahrbanoo karbalaee wrote: Dear justin In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please say me Is that correct. The definition of correct is up to you. I'll give you a few pointers (embedded below), but the leg-work of determining the validity of the parameters is your homework, not mine (or anyone else's!) title = cpeptide MD cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 5 ps. nstcomm = 1 nstxout = 50 nstvout = 0 Are you sure you don't want to save velocities every now and again? If your run crashes because of a hardware problem, you may want to be able to restart it... What about using nstxtcout? The output file will be greatly compressed relative to the .trr. It will save a lot of disk space when running analysis. nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 All of the parameters from nstlist to rvdw have values that are generally determined by the force field and its derivation scheme. Check the literature. ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein sol ref_t = 300 300 As long as you have no ions this is fine. ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 As long as you are expecting an NVT ensemble, this is also fine. ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Is this .mdp file for equilibration or production? You refer to it as the md.mdp, but if you're re-generating velocities, I certainly hope this .mdp file is for the beginning of equilibration. If you re-generate velocities repeatedly, then you don't get a continuous trajectory. -Justin -- 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling ([EMAIL PROTECTED])
Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? 1) I think there's an important distinction to be made here between accuracy and physical validity. If you use a thermostat, then the dynamic properties you obtain for the system will be different than the properties obtained without the thermostat, independent of what model you choose. So, I don't know that it's that useful to ask whether the differences from the true system due to thermostat are large compared to the differences due to the choice of model -- the results are going to be dependent on the thermostat, so the field has chosen a standard definition of the dynamics, one that most resembles the actual physical system (where there isn't temperature rescaling every 2 fs or a piston coupled to a 10 nm cube of water, etc). 2) If one uses the Berendsen thermostat, then statistical mechanics of canonical ensembles will not strictly apply, and one can't use many of the results one would like to (or, are using already incorrectly). One can do physics-based simulation of molecular models, or one can do non-physics-based simulations of molecular models. In many cases, the non-physics-based results will be statistically indistinguishable from the physics based results. But why bother with an uncontrolled approximation when you don't -have- to use one? It just adds another chance that what one simulates is not reproducible or reliable, and heaven knows that simulation currently has enough of those already. It's like building a tower out of blocks, and each uncontrolled approximation, no matter how small, is a bit of unevenness in the block. If you have just one wobbly block, you can stand on it pretty well -- you know the limits of the approximation, you can get a pretty good sense of what's going on with the system. Once there's a large number of wobbly blocks, though -- good luck standing on top of it and trying to build good science. As simulations get larger and more complicated, they are built out of more and more blocks, and we need to make sure we're paying careful attention to how well they all fit together. Best, Michael Shirts Research Fellow Columbia University Department of Chemistry ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling ([EMAIL PROTECTED])
Note that a recently a velocity rescaling algorithm was developed in the Parrinello group that does give the correct canonical ensemble. See: http://arxiv.org/abs/0803.4060. It might be nice to replace Berendsen with this algorithm, which should have the nice properties of Berendsen (converges to the constraint temperature quickly) without the serious drawbacks. Cheers, Michael On Wed, Jul 23, 2008 at 10:10 AM, Michael Shirts [EMAIL PROTECTED] wrote: Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? 1) I think there's an important distinction to be made here between accuracy and physical validity. If you use a thermostat, then the dynamic properties you obtain for the system will be different than the properties obtained without the thermostat, independent of what model you choose. So, I don't know that it's that useful to ask whether the differences from the true system due to thermostat are large compared to the differences due to the choice of model -- the results are going to be dependent on the thermostat, so the field has chosen a standard definition of the dynamics, one that most resembles the actual physical system (where there isn't temperature rescaling every 2 fs or a piston coupled to a 10 nm cube of water, etc). 2) If one uses the Berendsen thermostat, then statistical mechanics of canonical ensembles will not strictly apply, and one can't use many of the results one would like to (or, are using already incorrectly). One can do physics-based simulation of molecular models, or one can do non-physics-based simulations of molecular models. In many cases, the non-physics-based results will be statistically indistinguishable from the physics based results. But why bother with an uncontrolled approximation when you don't -have- to use one? It just adds another chance that what one simulates is not reproducible or reliable, and heaven knows that simulation currently has enough of those already. It's like building a tower out of blocks, and each uncontrolled approximation, no matter how small, is a bit of unevenness in the block. If you have just one wobbly block, you can stand on it pretty well -- you know the limits of the approximation, you can get a pretty good sense of what's going on with the system. Once there's a large number of wobbly blocks, though -- good luck standing on top of it and trying to build good science. As simulations get larger and more complicated, they are built out of more and more blocks, and we need to make sure we're paying careful attention to how well they all fit together. Best, Michael Shirts Research Fellow Columbia University Department of Chemistry ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to build boxes with constant number of solvent molecules?
Peyman Yamin wrote: Hello dears, I want to solvate different conformations of a molecule in a water box and I want to have the same number of solvent molecules in my box at the end. I do it with genbox but end up with different number of solvent molecules. A random insertion of more molecules results in a box which would not be easily equilibrated. I also tried to solvate in a larger box and then delete some molecules from the end of file so that I have a certain number of molecules for all of them, but it also results in a strange looking environments in the box which mostly lead to an equilibration crash. Does one know any practical strategy to solvate a molecule in a box and have the number of solvent molecules fixed?? I appreciate any suggestions, regards, Peyman genbox -maxsol -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
dear all, can anyone tell me how to install antechamber program on linux platform? From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
ANINDITA GAYEN wrote: dear all, can anyone tell me how to install antechamber program on linux platform? you are on the wrong mailing list for that. From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
On Tue, Jul 22, 2008 at 11:16:21PM -0400, [EMAIL PROTECTED] wrote: Thanks David for sharing your knowledge, especially the note that for further information one can refer to the literature that was written around the time that these thermostats were released. I have a question though: I was just trying to correct the impression from the posts that the issue with Berendsen is some urban legend - it is not and there is extensive literature on it - even if its not googleable by the way it is also true that if you use a thermostat or barostat then although long time averages are equivalent to averages in the NVT or NPT ensemble strictly the dynamics is no longer valid as a Newtonian trajectory so you should not derive dynamic properties from such trajectories. Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? I think the response by Michael says it as well as I could - this was a point made by some of these papers - so just because the averages are valid does not mean the dynamics is valid - you are right in that it may not be something that has an observable effect with current simulations but it is some form of artifact that may bias the simulations consistently whereas eg. with force fields you can have lots of cancellation of errors 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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS parameters for phosphotyrosine?
Dear All, Has anyone a topology for phosphorylated tyrosine residue in OPLS that can be shared? Sincerely, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85
___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 51, Issue 85
Dear justin thank you for your help and answer. about NVT or NPT,what is generally use for peptide?are there more different between them if iI can use NPT in our output(flexiblity)? AND about this file : it is md after equilbration. thanks again best regard karbalaee -- Message: 3 Date: Wed, 23 Jul 2008 18:14:50 +0430 From: shahrbanoo karbalaee [EMAIL PROTECTED] Subject: [gmx-users] Is it correct To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Dear justin In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please say me Is that correct. title = cpeptide MD cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 5 ps. nstcomm = 1 nstxout = 50 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein sol ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 -- 2)In the place program doesent have phrase for example PME,does. the gromacs use default? 3)when I use berendsen coupling is on and pcoup =yes and In my work is effect in fluctuate? best sh-karbalaee -- Message: 4 Date: Wed, 23 Jul 2008 13:54:57 + (GMT) From: Claus Valka [EMAIL PROTECTED] Subject: Re : [gmx-users] switch potential function gromacs 3.3.2 To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Dear Sir or Madam, For the version 3.3.2 the gromacs switch potential function is the following : Elja1 = (4.d0*eps1*sig1**6) * -(1.d0/r(i)**6) * (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5) Elja2 = (4.d0*eps1*sig1**12) * (1.d0/r(i)**12) * (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5) Switch = Elja1 + Elja2 Remarks: i) This is tested only when in the mdp file the vdw-type = Switch ii) The Elja1 is the dispersion part of the potential (not the force). iii) The Elja2 it the repulsion part of the potential (not the force). iv) eps is the value of epsilon and sig is the value of sigma v) r1 = rvdw-switch and rc1 = rvdw vii) The function of the manual that sais that it applies Phi(r) both on switch and shift option doesn't seem to apply in the switch case. vii) Someone can find out if someone searches at : a)/root/Desktop/software/gromacs/gromacs-3.3.2/src/mdlib/ b)The file is called tables.c c)look under if (bSwitch), where it sais swi d)for pow look at the beginning e)for Vtab under the cases etabLJ6 and etabLJ12 f)for whole under if ((r_r1) bSwitch) , that is the multiplication of the dispersion and repulsion part with swi g)in order to have units of energy someone must to multiply the above with 4*epsilon*sigma**6 for the dispersion part and 4*epsilon*sigma**12 for the repulsion part Yours Sincerely, Nikos __ Unglücklich mit Ihrer Mail-Adresse? Millionen neuer Mail-Adressen - jetzt bei Yahoo! http://de.docs.yahoo.com/mail/wunschmailadresse/index.html -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080723/fcb7a279/attachment-0001.html -- Message: 5 Date: Wed, 23 Jul 2008 09:58:14 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] new version of C terminus database for charmm To: sarbani chattopadhyay [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed sarbani chattopadhyay wrote: Hi, I am trying to run gromacs with charmm forcefield. # I had run the perl program convert_charmm_to_gromacs.pl and put the output files ffcharmmbon.itp and ffcharmmnb.itp into the gromacs
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
David Osguthorpe wrote: On Tue, Jul 22, 2008 at 11:16:21PM -0400, [EMAIL PROTECTED] wrote: Thanks David for sharing your knowledge, especially the note that for further information one can refer to the literature that was written around the time that these thermostats were released. I have a question though: I was just trying to correct the impression from the posts that the issue with Berendsen is some urban legend - it is not and there is extensive literature on it - even if its not googleable by the way it is also true that if you use a thermostat or barostat then although long time averages are equivalent to averages in the NVT or NPT ensemble strictly the dynamics is no longer valid as a Newtonian trajectory so you should not derive dynamic properties from such trajectories. Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? I think the response by Michael says it as well as I could - this was a point made by some of these papers - so just because the averages are valid does not mean the dynamics is valid - you are right in that it may not be something that has an observable effect with current simulations but it is some form of artifact that may bias the simulations consistently whereas eg. with force fields you can have lots of cancellation of errors Cancellation of errors is not an excuse for poor force fields. In addition, built-in cut-offs for some force fields also give systematic bias, but this is beside the point. Although it is indeed well-known that Berendsen thermostat (and Barostat!) create significant artifacts, these are not as bad as they used to be, in particular due to the use of PME. Temperature coupling hardly does anything at all when using PME, which you can verify by plotting the temperature scaling factor as a function of time. So we are all waiting for a healthy volunteer to implement the latest and greatest algorithms in the latest and greatest gromacs development code. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Membrane: anisotropic pressure coupling
Hello, I am new in Gromacs, and I am trying to simulate the interaction between a DOPC membrane and a protein. I have equilibrated my system at constant volume and now I would like to switch to constant pressure. I think the best option for me is to use ANISOTROPIC pressure, because I want to study the ondulations produced in the membrane due to the protein. Do you recommend anisotropic pressure for this? or semiisotropic would be enough? Another question is about the values of tau_p and ref_p. I have read in the manual that in the case of anisotropic pressure I should use 6 values. Which values do you recommend to use? Should I use also 6 values for compressibility and ref_p? Pcoupl = BerendsenPcoupltype = anisotropictau_p = 2.0 2.0 2.0 2.0 2.0 2.0compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-54.5e-5ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 Thank you very much for your help in advance. Best wishes, Rebeca García FandiñoParc Cientific de [EMAIL PROTECTED] _ Sigue en directo todas las competiciones deportivas en MSN Deportes http://deportes.es.msn.com/___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE:[gmx-users] cannot print velocity information to trr/xtc files (Carbon Nanotube inside water)
I am to accelerate water while freezing another group and would like to know velocity information as has been posted before and was wondering if a solution to the problem has been found. Andy Nadir Kaplan wrote: What is going on here? How can I get velocity info? Any help will be greatly appreciated. Note that, there is an external acceleration on the water molecules, where is the position of CNT is fixed. So obviously water molecules should have finite velocities. Turn off the weird stuff (freeze groups and accelerate groups) until you've got your basic issues sorted out. MD simulations in general and CNT simulations in particular are not easy things to do right. Learn to walk before you try to run! :-) Freezing is for simplicity. One needs velocity to run. Yeah, but freezing and accelerating do things to velocities. If you're having problems, a good strategy is to simplify the situation until you can identify where the problem arises... thus, no freezing and accelerating. Below I paste another mdp file which I used for the MD part of the same simulation. That MD simulation was succesfully over and I was able to reproduce some results in the literature by using position info. Again, in the .trr file of that simulation, there are no velocities. Well, those reproduced results probably mean that there *were* velocities :-) Velocities must be there in the .trr for the last timestep, so long as mdrun was allowed to terminate normally. If you really had nstvout = 5000 and you are looking at the correct non-post-processed trajectory with gmxdump on a suitable timestep, then your observations are inexplicable, unless there's some weird gotcha with no velocities being written for atoms in either a freeze or accelerate group... not that that makes much sense... In short, it seems much more likely you've made an error than that there's a weird bug. My earlier advice is still good - get a clean working directory and do the same kind of simulation but without the freeze and accelerate groups and see if you can reproduce your problem while recording everything you did on the way. If it now works, do the same but add in the weird stuff until you isolate the problem - if any. Good luck! 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Hi all, One of the conceptual difference between Berendsen and Nose-Hoover (NH), is the following. NH is basically a second order relaxation to the target temperature, which implies an oscillatory behavior. Berendsen is a first order relaxation (exponential type of behavior). This is preferable when the initial temperature is far from the target temperature, in which case NH is likely to produce large oscillations and, in general, take longer to equilibrate. Hence the practice to use Berendsen for the first part of the equilibration, and NH for production. There are still papers published on the subject in the alive literature. For example there is an analysis of the Berendsen dynamics in Morishita, JCP 113 (8) : 2976 (2000) In short, he finds approximate expressions for the configurational part of the state distribution function. It essentially varies between canonical for exceedingly small time constants (of the order of the timestep) to microcanonical for very large time constants. The distribution of momenta remains unknown. In addition to the average temperature, the temperature fluctuations expected for the NVT ensemble must be reproduced in the simulation. Nose-Hoover was shown to do this correctly. This could be important when studying the stability of a conformation for example. Now concerning Chris' question: [EMAIL PROTECTED] wrote: Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? There are two aspects here: (a) point charges and LJ force, which constitute the physical model, and (b) the cutoffs and such, which are simulation artefacts and disrupt the physics of the model (by allowing creation of energy, etc...). My opinion is that, given a physical model (even approximate), one should simulate the dynamics as accurately as possible, in order to produce the thermodynamical ensemble corresponding to the underlying physical model. Before plugging in the thermostat, one should check that the simulation conserves energy not too bad(using PME or switch functions, etc...). Now if there is still an energy drift, the thermostat will absorb the excess energy, and the system will end up in a non-equilibrium steady state, with a heat well (cutoffs, etc) and a heat sink (thermostat). The good side is that the NH thermostat was shown (by Hoover himself) to produce a stationary canonical distribution even in a non-equilibrium case. Sorry for the long email :) Michel -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland http://ludwig-sun1.unil.ch/~mcuendet == ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 51, Issue 85
shahrbanoo karbalaee wrote: Dear justin thank you for your help and answer. about NVT or NPT,what is generally use for peptide?are there more different between them if iI can use NPT in our output(flexiblity)? There is no substitute for a thorough examination of the literature. AND about this file : it is md after equilbration. Then gen_vel = yes just negated your equilibration. Whether or not that will cause any problems will become obvious if your simulation crashes. -Justin thanks again best regard karbalaee -- Message: 3 Date: Wed, 23 Jul 2008 18:14:50 +0430 From: shahrbanoo karbalaee [EMAIL PROTECTED] Subject: [gmx-users] Is it correct To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Dear justin In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please say me Is that correct. title = cpeptide MD cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 5000 ; total 5 ps. nstcomm = 1 nstxout = 50 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein sol ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 -- 2)In the place program doesent have phrase for example PME,does. the gromacs use default? 3)when I use berendsen coupling is on and pcoup =yes and In my work is effect in fluctuate? best sh-karbalaee -- Message: 4 Date: Wed, 23 Jul 2008 13:54:57 + (GMT) From: Claus Valka [EMAIL PROTECTED] Subject: Re : [gmx-users] switch potential function gromacs 3.3.2 To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Dear Sir or Madam, For the version 3.3.2 the gromacs switch potential function is the following : Elja1 = (4.d0*eps1*sig1**6) * -(1.d0/r(i)**6) * (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5) Elja2 = (4.d0*eps1*sig1**12) * (1.d0/r(i)**12) * (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5) Switch = Elja1 + Elja2 Remarks: i) This is tested only when in the mdp file the vdw-type = Switch ii) The Elja1 is the dispersion part of the potential (not the force). iii) The Elja2 it the repulsion part of the potential (not the force). iv) eps is the value of epsilon and sig is the value of sigma v) r1 = rvdw-switch and rc1 = rvdw vii) The function of the manual that sais that it applies Phi(r) both on switch and shift option doesn't seem to apply in the switch case. vii) Someone can find out if someone searches at : a)/root/Desktop/software/gromacs/gromacs-3.3.2/src/mdlib/ b)The file is called tables.c c)look under if (bSwitch), where it sais swi d)for pow look at the beginning e)for Vtab under the cases etabLJ6 and etabLJ12 f)for whole under if ((r_r1) bSwitch) , that is the multiplication of the dispersion and repulsion part with swi g)in order to have units of energy someone must to multiply the above with 4*epsilon*sigma**6 for the dispersion part and 4*epsilon*sigma**12 for the repulsion part Yours Sincerely, Nikos __ Unglücklich mit Ihrer Mail-Adresse? Millionen neuer Mail-Adressen - jetzt bei Yahoo! http://de.docs.yahoo.com/mail/wunschmailadresse/index.html -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080723/fcb7a279/attachment-0001.html -- Message: 5 Date: Wed, 23 Jul 2008 09:58:14 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] new version of C terminus database for charmm To: sarbani chattopadhyay [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed sarbani chattopadhyay wrote: Hi, I am trying to run gromacs with charmm
Re: [gmx-users] Membrane: anisotropic pressure coupling
Rebeca García Fandiño wrote: Hello, I am new in Gromacs, and I am trying to simulate the interaction between a DOPC membrane and a protein. I have equilibrated my system at constant volume and now I would like to switch to constant pressure. I think the best option for me is to use ANISOTROPIC pressure, because I want to study the ondulations produced in the membrane due to the protein. Do you recommend anisotropic pressure for this? or semiisotropic would be enough? A good discussion of such topics can be found in: Kandt, et al. (2007) Methods 41: 475-488. Another question is about the values of tau_p and ref_p. I have read in the manual that in the case of anisotropic pressure I should use 6 values. Which values do you recommend to use? Should I use also 6 values for compressibility and ref_p? Pcoupl = Berendsen Pcoupltype = anisotropic tau_p = 2.0 2.0 2.0 2.0 2.0 2.0 Only one value of tau_p is necessary. compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-54.5e-5 Setting the off-diagonal compressibilities as such may lead to deformations of the box. From the manual: When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. Beware that anisotropic scaling can lead to extreme deformation of the simulation box. ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 Similarly, you are specifying a pressure in the diagonal directions (the last three values). -Justin Thank you very much for your help in advance. Best wishes, Rebeca García Fandiño Parc Cientific de Barcelona [EMAIL PROTECTED] ¡El Mundo Messenger te espera! Entra ya en I love Messenger y descubre las últimas novedades, trucos, emoticonos. Entra ya en I love Messenger http://www.vivelive.com/ilovemessenger/ ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topologies from autodock
KAUSHIK H.S. wrote: hi, I have got a docked complex (ligand and protein) in pdb format from autodock. I am unable to generate topoloy file for the docked complex, (but, I can do the same for protein and ligand separately). Can any of you please guide me in generating topoloy file for the docked complex. Let me be more candid, I am novice in this field. Generally, if this is the case, the answer can be found in one of the following sources: 1. The list archive 2. The wiki site 3. Google In your case, you can quickly use Option #3 to locate John Kerrigan's enzyme-ligand tutorial. -Justin regards, Kaushik Bring your gang together. Do your thing. Find your favourite Yahoo! Group. http://in.rd.yahoo..com/tagline_groups_9/*http://in.promos.yahoo.com/groups/ ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -pbc cluster with -center in trjconv 3.3.1
Hello, I have a DPC micelle in a rhombic dodecahedron. I want to use the pull code relative to the center of mass of the micelle and therefore I need to keep all detergent monomers in the same periodic image (otherwise I suspect that the COM will be calculated incorrectly). My problem is that I can not seem to get all of the detergent monomers into the center of a triclinic unit cell. It doesn't even need to be the center, just far enough from an edge that all detergents will be interpreted as being in the main unit cell by grompp or perhaps by mdrun in the very first timestep. Once I have this representation, I can use one pull restraint in absolute coordinates to keep the micelle in the unit cell and another pull restraint to do something more interesting. I have been unable to get the representation that I am looking for in gromacs-3.3.1. I realize that gromacs-3.3.3 has an enhanced trjconv suite, but the -pbc cluster option in 3.3.3 and 3.3.2 sends me into an infinite loop and without the cluster option the -center option does not maintain the micelle (i.e. detergent monomers are distributed to the corners of the unit cell.) I acknowledge the infinite reality of PBC, but I'll emphasize that my concern here is proper COM treatment. From looking at the source code it appears that the pull code is smart enough to look back to the initial frame and put things in the original box, but still I need to generate the correct starting frame. To be clear about the infinite loop that I get for 3.3.2 and 3.3.3, here is some output: $ ../../../../exe/gromacs-3.3.3_newccb/exec/bin/trjconv -f 100ns.gro -o 100ns_trjconv.gro -pbc cluster -s tpr/empty.tpr Will write gro: Coordinate file in Gromos-87 format Reading file tpr/empty.tpr, VERSION 3.3.1 (single precision) Reading file tpr/empty.tpr, VERSION 3.3.1 (single precision) Select group for clustering Opening library file /home/cneale/gromacs/oplspope.top/aminoacids.dat Group 0 ( System) has 29870 elements Group 1 ( DPC) has 1150 elements Group 2 ( SOL) has 28720 elements Select a group: 1 Selected 1: 'DPC' Select group for output Opening library file /home/cneale/gromacs/oplspope.top/aminoacids.dat Group 0 ( System) has 29870 elements Group 1 ( DPC) has 1150 elements Group 2 ( SOL) has 28720 elements Select a group: 0 Selected 0: 'System' COM:0.144 0.000 0.000 iter = 1 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 2 Isq = 521.888 COM:0.144 0.000 0.000 iter = 3 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 4 Isq = 521.888 COM:0.144 0.000 0.000 iter = 5 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 6 Isq = 521.888 COM:0.144 0.000 0.000 iter = 7 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 8 Isq = 521.888 COM:0.144 0.000 0.000 iter = 9 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 10 Isq = 521.888 COM:0.144 0.000 0.000 iter = 11 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 12 Isq = 521.888 COM:0.144 0.000 0.000 iter = 13 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 14 Isq = 521.888 COM:0.144 0.000 0.000 iter = 15 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 16 Isq = 521.888 COM:0.144 0.000 0.000 iter = 17 Isq = 353349.094 COM:3.672 3.528 4.600 iter = 18 Isq = 521.888 COM:0.144 0.000 0.000 iter = 19 Isq = 353349.094 . Thanks if anybody has some good ideas about how I might proceed. Chris. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
