[gmx-users] help
HI can any one help me queries? 1) what and all are the essential file required for adding a solvent and run a MD? (i am not looking for the stnd solvents , ( as given in top or tutor) ,) 2) can u pleae tell me in steps ? vinod ___ 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] help
vinod kumar wrote: HI can any one help me queries? 1) what and all are the essential file required for adding a solvent and run a MD? (i am not looking for the stnd solvents , ( as given in top or tutor) ,) 2) can u pleae tell me in steps ? There's tutorial material available on the GROMACS website http://www.gromacs.org/. Please use it. There's also a lot of information on the GROMACS wiki http://wiki.gromacs.org. You should have a read of this web page, to learn how to ask smarter questions... http://www.catb.org/~esr/faqs/smart-questions.html 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] free energy perturbations and B-parameter specifications
Hi You have to be more specific... Did you just do one sim for Gly-Ala? Are you sure, you did the simulations in a way, you can compare it to exp. results? (think about doing the perturbation once in water and once in vacuum or so) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Soren Enemark wrote: Dear Gromacsers, I have been doing free energy perturbations Gly-Ala in one strand of collagene. Now, the problem is that I have later closely reread the section 5.6.4 (Free Energy Calculations) p. 105 in which it says: Bonded interactions between atoms that are not perturbed do not need B parameter specifications ... My questions are: 1. Does this mean that bonded interactions between atoms that ARE perturbed DO need B parameter specifications? Even if they are the same in state A and B? 2. What about the other topology parameters (angles, dihedrals etc), do they need to be specified too? 3. What happens if I have not specified these specifications? The relevant parts of the topology file which I use are: [ atoms ] 87 N 13ALA N 49 -0.2814.0067 ; qtot 0.72 88 H 13ALA H 49 0.28 1.008 ; qtot 1 89CH2 13ALA CA 50 0 14.027 CH1 0.0 3.019 ; qtot 1 90DUM 13ALA CB 50 0 15.035 CH3 0.0 15.035 ; qtot 1 91 C 13ALA C 51 0.38 12.011 ; qtot 1.38 92 O 13ALA O 51 -0.3815.9994 ; qtot 1 ... [ bonds ] ... 8789 2gb_20 8990 2gb_26 8991 2gb_26 ... [ angles ] 858789 2ga_30 888789 2ga_17 878990 2ga_12 878991 2ga_12 908991 2ga_12 899192 2ga_29 899193 2ga_18 And so on, ie, no B specifications have been done except for the atoms! Best regards, and thank you in anticipation, Soren Ps. One (non-gromacs -sorry) question, given that the above is not wrong: For the pertubation Gly-Ala I have get a deltaG of 0.8 kcal/mol. Looking through literature, this does not seem all wrong, say if the pertubation took place in an alpha-helix. On the other hand, it is close to the thermal energy (~kT), and a previous article doing the exact same perturbation arrives at a deltaG around 8.6 kcal/mol. Could anyone comment on that? Alt i én. Få Yahoo! Mail http://dk.mail.yahoo.com med adressekartotek, kalender og notesblok. ___ 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 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] Mutagenesis
Hi The question arises, is physically acceptance equal to biological reality and the answer is (with reasonable probability) no. What I suppose, you want to do is calculating the affinity difference (free energy difference) for binding of a slab of DNA to a protein with mutated aminoacids. Therefore you will calculate via TI or so the difference in free energy of two states, where A is the one with the original AA and B with the mutated AA. With GROMACS, you can morph between these states and calculate the DeltaG. To get the atoms of the B-state positioned correctly, you may setup a library of your AAs and fit the backbone atoms to the BB-atoms of the original one. Then you have more or less reasonable positions for you B-state side-chain atoms. Afterwards have a look which side chain atoms of the B-state AA you really have to grow and afterwards start the sim. Which kind of TI one should use is hard to say, but I'd suggest discrete TI (not slow growth), because your B-state has the time to equilibrate (more or less) properly. If all this is feasible, one probably can't answer. At last, that's the best one can doand, btw., expect to invest some time to get this working. Hope, this helps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Esther Caballero-Manrique wrote: Hi everyone, I am new to mutagenesis studies, so I was wondering if I could get some input on my approach. My task involves mutagenizing a residue (with all 19 possibilities) in a protein that binds DNA, and then deciding whether the resulting structure is physically acceptable. My approach to do this is 1) mutate using MODELLER, 2) check the structure with something like PROCKECK (although since I am just mutating one residue, this doesn't seem important/useful), 3) align the resulting structure from MODELLER with the original and paste the DNA 4) check for clashes with PROCHECK, and 5) do MD to see whether the model is feasible/calculate free energy of binding. Obviously all steps are easy and fast except the last one, and my question is, does anyone think that step 5 is overdoing it if one just needs to know whether a structure is feasible ( i.e., I am not using MD for refinement, but as a check of the feasibility of the complex)? Does anyone have a better/easier way to do this? Thanks a lot for your help, Esther -- Esther Caballero-Manrique Unit of Cancer Pathology Center for Excellence in Research on Aging University G. D' Annunzio Via Colle dell' Ara 66013 Chieti Scalo (Chieti), Italy ___ 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 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] dummy atom definition prob in FEP
Friend... What are you trying to do??? If you want to do standard FEP with growing something into dummy (NOT virtual site) or from dummy, you must not use virtual sites! Virtual sites in fact, have no mass; neither in A- nor in B-state. Please read the fManual about virtual particles, their usage and why they exist in GROMACS (hint, delocalized charge) As far as I know, you can't morph a virtual site to a real particle. I also think, It wouldn't make much sense, though. If you want to morph away e.g. a proton, define a dummy in the b-state, which has no LJ parameters (eps and sigma=0) and no charge, but still the original mass. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi, Thanks for reply. It seems that specifying mass_B = mass_A doesn't help to solve the problem. However, if I don't use the directory [virtual_site#] the errors disappear! What's the result if I do this? Is the directory necessary in the FEP calculation to define the dummy atoms? Thanks, Qin On 7/20/07, *Stéphane Téletchéa* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Wang Qin a écrit : Hi there, I have a problems when I do a FEP calculation. Below is how I defined dummy atoms in the topology file: [atom] ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_1721 LG6 H21 21 0.4650 1.00800 opls_0 0. 0.00 22 opls_1721 LG6 H22 22 0.4650 1.00800 opls_0 0. 0.00 .. I think you need to specify the mass_B=mass_A, at least this is how it is setup in the tutorials i've done (the one from Berk Hess and the other one from David Mobley). I've also done calculations without setting the mass for B (like you did) and did not encounter any problem, the error you're seing could thus come from another part of your system. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ 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 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] mailto:[EMAIL PROTECTED]. 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf and the placement of the center of mass
Hi Arneh, From the help of editconf (editconf -h) you could have seen that it has no such option. It wouldn't be very hard to add it though... Cheers, Tsjerk On 8/8/07, Arneh Babakhani [EMAIL PROTECTED] wrote: Hi, In editconf, there's an option -center which allows you to place the geometrical center of your molecular at a desired location. I was wondering, is there an analogous option for the placement of the center of mass of a molecule? Thanks, Arneh ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Constrains and TI
Hi First, for the other topic you posted (which is probably somehow related to this one): Now, please be more specific with what you want to doYou wrote: What I want to do is calculate the free energy difference of pulling the ligand away from the receptor This is a pulling approach, where you would like to do AFM sims and afterwards use Jarzynski. If that is what you want, search the literature for Jarzynski and try to understand his theorem (you will see, one pulling sim is not enough for free energy calc). Then you wrote: I want to do it using theromdynamic intergration using the Lamda 0/1 stuff This is a totally different approach With both, you can ESTIMATE binding free energies. Still, both are very different in the way to setup a simulation in GROMACS. You WILL find out, how to do it by: 1. Reading the manual 2. Searching the mailing list 3. Using the GROMACS Wiki 4. Using some of the tutorials, which were posted, by e.g. David Mobley Now, coming to your idea about using distance restraints to pull the ligand away (its more of a push). I think (correct me if I'm wrong), that you can't use A and B state distance restraints in GROMACS (or better say, they will stay the same for both states). I'd suggest to use either TI OR AFM pulling. For sure, you could do both and see, if you get similar free energy differences with both methods... I don't think, you can calculate the free energy difference by using different distance restraints, anyway. Regards P.S. As I just saw it. Inform yourself about the difference between CONSTRAINTS and RESTRAINTS (there is an important one...) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: hello all, is it possible to constrain a distance (or several) between a ligand-receptor complex inorder to simulate free energy change of separating the ligand from the receptor? I intend to use TI and lamda to do free energy calculations. any help is appreicated. Belquis ___ 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 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] Continuation diferent machine.
Thank you Erick for your rapidly responce. On Tuesday 07 August 2007 7:58 pm, Erik Lindahl wrote: Binary identical means that the files are identical bit-for-bit, i.e. if you ran cmp traj1.trr traj2.trr it would report the files to be the same/indistinguishable. This is normally only important for debugging. If you don't know it doesn't apply to you :-) All that matters for you is that 3.3 = 3.2, so it should work fine; the hardware doesn't matter. Cheers, Erik On Aug 8, 2007, at 12:25 AM, Anthony Cruz wrote: Hi Erick, Thank you for you responce. I am sorry but I dont unterstand the term _binary_ identical results. The first simulation was run on a linux machine (pentium 4) with gromacs 3.2 from the rpm included in suse. The new machine will be (Pentium4 Xeon) with gromacs 3.3 (manual compiled) with SDSCs Rocks clustering system. I think that the architecturesare more or less the same. I am correct??? So I could continue the job in the new machine??? Best Regards, Anthony On Tuesday 07 August 2007 5:25 pm, Erik Lindahl wrote: Hi Anthony, As long as the version you're continuing with is the same or more recent than the one you started with it should work fine; all gromacs output files are stored in portable formats and are can be read by newer versions. You are not guaranteed _binary_ identical results, though - that depends on the compiler, or if you are running on architectures where we use tuned assembly loops. Cheers, Erik On Aug 7, 2007, at 10:57 PM, Anthony Cruz wrote: Hi users: I have made some simulation in one of our workstation. Now I want to extend the simulations few nanoseconds. I can continue the simulations in other machine without affecting the results? I need to use the same gromacs version? Best Regards, Anthony ___ 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 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 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 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 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] dummy atom definition prob in FEP
Thank you, Maik. I do want to do standard FEP and thank you for telling me that FEP don't go with virtual sites. It does help. BTW, may I ask you why I should define a none_zero mass for a dummy atom? Thanks, Qin On 8/8/07, Maik Goette [EMAIL PROTECTED] wrote: Friend... What are you trying to do??? If you want to do standard FEP with growing something into dummy (NOT virtual site) or from dummy, you must not use virtual sites! Virtual sites in fact, have no mass; neither in A- nor in B-state. Please read the fManual about virtual particles, their usage and why they exist in GROMACS (hint, delocalized charge) As far as I know, you can't morph a virtual site to a real particle. I also think, It wouldn't make much sense, though. If you want to morph away e.g. a proton, define a dummy in the b-state, which has no LJ parameters (eps and sigma=0) and no charge, but still the original mass. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi, Thanks for reply. It seems that specifying mass_B = mass_A doesn't help to solve the problem. However, if I don't use the directory [virtual_site#] the errors disappear! What's the result if I do this? Is the directory necessary in the FEP calculation to define the dummy atoms? Thanks, Qin On 7/20/07, *Stéphane Téletchéa* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Wang Qin a écrit : Hi there, I have a problems when I do a FEP calculation. Below is how I defined dummy atoms in the topology file: [atom] ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_1721 LG6 H21 21 0.4650 1.00800 opls_0 0. 0.00 22 opls_1721 LG6 H22 22 0.4650 1.00800 opls_0 0. 0.00 .. I think you need to specify the mass_B=mass_A, at least this is how it is setup in the tutorials i've done (the one from Berk Hess and the other one from David Mobley). I've also done calculations without setting the mass for B (like you did) and did not encounter any problem, the error you're seing could thus come from another part of your system. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ 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 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] mailto:[EMAIL PROTECTED]. 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dummy atom definition prob in FEP
Your system will explode. Actually I'm not sure, why that is, but probably, because some forces from the bonded terms are transferred to your mass-zero particle, which then accelerates infinitly fast...even though I would expect some division over zero error in the velocity calculation... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Thank you, Maik. I do want to do standard FEP and thank you for telling me that FEP don't go with virtual sites. It does help. BTW, may I ask you why I should define a none_zero mass for a dummy atom? Thanks, Qin On 8/8/07, *Maik Goette* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Friend... What are you trying to do??? If you want to do standard FEP with growing something into dummy (NOT virtual site) or from dummy, you must not use virtual sites! Virtual sites in fact, have no mass; neither in A- nor in B-state. Please read the fManual about virtual particles, their usage and why they exist in GROMACS (hint, delocalized charge) As far as I know, you can't morph a virtual site to a real particle. I also think, It wouldn't make much sense, though. If you want to morph away e.g. a proton, define a dummy in the b-state, which has no LJ parameters (eps and sigma=0) and no charge, but still the original mass. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi- bpc.mpg.de http://bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi, Thanks for reply. It seems that specifying mass_B = mass_A doesn't help to solve the problem. However, if I don't use the directory [virtual_site#] the errors disappear! What's the result if I do this? Is the directory necessary in the FEP calculation to define the dummy atoms? Thanks, Qin On 7/20/07, *Stéphane Téletchéa* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Wang Qin a écrit : Hi there, I have a problems when I do a FEP calculation. Below is how I defined dummy atoms in the topology file: [atom] ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_1721 LG6 H21 21 0.4650 1.00800 opls_0 0. 0.00 22 opls_1721 LG6 H22 22 0.4650 1.00800 opls_0 0. 0.00 .. I think you need to specify the mass_B=mass_A, at least this is how it is setup in the tutorials i've done (the one from Berk Hess and the other one from David Mobley). I've also done calculations without setting the mass for B (like you did) and did not encounter any problem, the error you're seing could thus come from another part of your system. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: gmx-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 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] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] Timestep
Thank a lot to all for your inputs.. Ramya. Hi, In principle Gromacs should never just crash with a segmentation fault, but at least give you a (perhaps cryptic) error message and exit somewhat gracefully. As far as I know there is only one exception to this: If you are using tabulated interactions the table can only be of finite size, and thus there will be a cutoff beyond which there is no data. Unfortunately it is not possible to determine this automatically, so you have to set the table extension beyond your normal cutoffs in the mdp file (table-ext). The obvious question is of course why we don't do a check for the distance before the table lookup, but that would be a conditional statement in the very innermost nonbonded loop, and drastically reduce performance. I don't think your system will explode completely with 3fs steps though, so the best options might be to compile with debug flag (./ configure CFLAGS=-O3 -g) and run the simulation in a debugger to see where it crashes. Cheers, Erik On Aug 7, 2007, at 8:30 PM, Xavier Periole wrote It is not possible to answer your question from the information you give. A lot of things can cause a segmentation fault. From compilation to your particular system. Put a search on the user-list, you'll get an idea of possible problems. It depends what you will be looking at but I would suggest to stick to a 2 fs time step. XAvier Thanks to Xavier for his prompt reply.. Actually my objective is a bit longer[50-60ns] but the problem is that even if i cant change the time-step to 0.003 it is exiting saying segmentation fault then how is it possible with 1fs [or 4 fs as suggested] which i want to do to reduce time. I wanted to know where the problem is... why cant i increase the time step and the only error shown is 'segmentation fault'..so is the reason in compilation or coding or machine precision or is it with molecular system wise thats what i was trying to understand.. Thanks again.. Ramya. 10 ns of a solvated protein of regular size should not require much computing time. Increasing the time-step above 2 fs is a solution to increase the speed of the run but then you face the problem of not integrating the fast movement correctly and this can end up in large forces and then you run crashes. You could use dummy hydrogens (see manual) and heavy water and use a 4 fs time step. This is ok for a simple protein in a box of water. But again 10ns of a protein solvated is not a long simulation. XAvier I am trying to perform a simulation run of 10ns for my system [protein+waterbox].The system works fine if i use timestep[dt=0.002 fs]. To balance the run time and time-consumption, when we try a .mdp file with slight increase of timestep i.e., to 0.003 fs; grompp works fine and generates input tpr, but when going further with mdrun, the program crashes, giving error: Segmentation Fault So i have to increase the number of steps[nsteps] to achieve required run time.But this'll be time consuming.I am unable to figure out any alternative. I am using Gromacs 3.3 on IBM Power5 machine with SLES9. Please suggest me the required to be done.Thanks in advance. The .mdp file i've used: integrator = md ;Total simulation time: 5000 ps :time step in femtoseconds dt = 0.002 ;number of steps nsteps = 250 nstxout = 100 nstvout = 100 nstlog = 10 nstenergy= 10 nstxtcout= 10 ;xtc_grps= prot ;group(s) to write to energy file energygrps = protein non-protein Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 10 cut-off distance for the short-range neighbor list rlist= 0.8 ;treatment of electrostatic interactions coulombtype = PME rcoulomb = 0.9 *$$$* Ramya Cherukupalli, Final year, M.S Bioinformatics, IIIT - H. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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 - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole -
Re: [gmx-users] Constrains and TI
Thank you for the reply, Sorry for the confusion of my two emails. I guess I was using the word pulling in the wrong context. Now after my extensive reading, what I meant is that i want to calculate the absoulte binding free energy of a ligand/receptor complex. I have read the manual over and looked at the tutorials, and came to the idea that i can constrain distances b/w the ligand and the receptor and input a distance for state B to vary the distance using lamda. (Manual 3.3 chapter 6 special topics, section 6.3 Calcuating the PMF using the free-energy code) I am using contraints type 2, which can be perturbed in free energy calculations. here is what I used in my calculation: [ constraints ] ; ai aj funct length_A length_B 44 258 2 0.2592.406 123 179 2 0.3292.334 I am currently running a 5ns using the slow-growth method to give me an idea of what happens to the system. I am also looking into using orientational-restrains and using a thermodynamic cycle instead of PMF of the unbinding of the ligand to receptor. please correct me if I am wrong. and thanks for ur help. Belquis Hi First, for the other topic you posted (which is probably somehow related to this one): Now, please be more specific with what you want to doYou wrote: What I want to do is calculate the free energy difference of pulling the ligand away from the receptor This is a pulling approach, where you would like to do AFM sims and afterwards use Jarzynski. If that is what you want, search the literature for Jarzynski and try to understand his theorem (you will see, one pulling sim is not enough for free energy calc). Then you wrote: I want to do it using theromdynamic intergration using the Lamda 0/1 stuff This is a totally different approach With both, you can ESTIMATE binding free energies. Still, both are very different in the way to setup a simulation in GROMACS. You WILL find out, how to do it by: 1. Reading the manual 2. Searching the mailing list 3. Using the GROMACS Wiki 4. Using some of the tutorials, which were posted, by e.g. David Mobley Now, coming to your idea about using distance restraints to pull the ligand away (its more of a push). I think (correct me if I'm wrong), that you can't use A and B state distance restraints in GROMACS (or better say, they will stay the same for both states). I'd suggest to use either TI OR AFM pulling. For sure, you could do both and see, if you get similar free energy differences with both methods... I don't think, you can calculate the free energy difference by using different distance restraints, anyway. Regards P.S. As I just saw it. Inform yourself about the difference between CONSTRAINTS and RESTRAINTS (there is an important one...) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: hello all, is it possible to constrain a distance (or several) between a ligand-receptor complex inorder to simulate free energy change of separating the ligand from the receptor? I intend to use TI and lamda to do free energy calculations. any help is appreicated. Belquis ___ 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 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 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] Using editconf to center on 0 0 0 , then using genbox
Hi, I'm using editconf to center my sytem about the origin (0 0 0). No problem there. But then when I use genbox to solvate the resulting structure, the solvent is offset (not centered about 0 0 0). Is there a way to correct this? Arneh ___ 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] problems with parallel mdrun
Dear gmx users, I am using a current CVS version of Gromacs and using the newly introduced options for simulations with walls. I am facing the following two problems. I get the following errors while using paralled version of mdrun compiled with openmpi. mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1 * Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 Source code file: gmx_parallel_3dfft.c, line: 90 Fatal error: nx (50) and ny (50) must be divisible by the number of nodes (4). *** I am using a cubic box of 5nm and grid spacing is 0.1. The simulations runs fine if i use 5 nodes I am using a machines with 2 dual xeon processors so -np 4 is more appropriate for my sytems. Is there any way to use -np 4 without changing the gridspacing or box size? second question is regarding wall_denstiy option. As i understood from the manual the wall density is a number density in units of number/nm2 in case of 10-4 potential and is number/nm3 in case of 9-3 potential. please correct me if i am wrong. Thank you in advance With Regards, Gurpreet ___ 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] pressure scaling more than 1%
Dear all, I am trying to do a FEP. In the equilibrium step, it fails after about 500 steps with a warnning: pressure scaling more than 1%, mu: 1.06718 1.06718 1.06718. I searched the old discussion about it and then try to increase the tau_p to 2 till 10. But it just goes futher but still meets the problem at the end. Any idea about it? Regards, Qin ___ 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] Using editconf to center on 0 0 0 , then using genbox
Arneh Babakhani wrote: Hi, I'm using editconf to center my sytem about the origin (0 0 0). No problem there. But then when I use genbox to solvate the resulting structure, the solvent is offset (not centered about 0 0 0). Is there a way to correct this? Have you tried editconf on the solvated structure? Why does it matter anyway? 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] problems with parallel mdrun
Gurpreet Singh wrote: Dear gmx users, I am using a current CVS version of Gromacs and using the newly introduced options for simulations with walls. I am facing the following two problems. You should send separate emails for each problem, with different subject headings, so that people with relevant expertise have the maximum chance of seeing your problem. The second problem here has nothing to do with your email subject line... I get the following errors while using paralled version of mdrun compiled with openmpi. mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1 * Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 Source code file: gmx_parallel_3dfft.c, line: 90 Fatal error: nx (50) and ny (50) must be divisible by the number of nodes (4). *** I am using a cubic box of 5nm and grid spacing is 0.1. The simulations runs fine if i use 5 nodes I am using a machines with 2 dual xeon processors so -np 4 is more appropriate for my sytems. Is there any way to use -np 4 without changing the gridspacing or box size? No. I'm guessing your .mdp file is trying to specify nx/ny/nz, rather than the grid spacing. If you specify the latter, grompp will take care of this issue so that you get the largest allowable spacing smaller than (or equal to) the requested grid spacing. second question is regarding wall_denstiy option. As i understood from the manual the wall density is a number density in units of number/nm2 in case of 10-4 potential and is number/nm3 in case of 9-3 potential. please correct me if i am wrong. I don't know. 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] Using editconf to center on 0 0 0 , then using genbox
I'd like to have my structure centered on 0 0 0 . The solvated structure is completely off. My protein is at the center, but the solvation shell is way off center. I just dont understand why genbox isn't recognizing the previous editconf step. Ok, I'll try solvating first then using editconf. Arneh Babakhani wrote: Hi, I'm using editconf to center my sytem about the origin (0 0 0). No problem there. But then when I use genbox to solvate the resulting structure, the solvent is offset (not centered about 0 0 0). Is there a way to correct this? Have you tried editconf on the solvated structure? Why does it matter anyway? 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 ___ 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] Suggestion needed for new workstation
Hi, everybody. I want to buy a new workstation for MD simulation. I think the Mac Pro from Apple is really nice. The configuration: *Two 3.0GHz Quad-Core Intel Xeon * *8GB (4 x 2GB) * *500GB 7200-rpm Serial ATA 3Gb/s with price: *$6,225.00 Any suggestions or comments? Thanks in advance. * *-- Sincerely yours, James Jianzhang ___ 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] g_energy and pressure
I am trying to analyze the pressure of my box with respect to time using g_energy but it seems to give crazy numbers. For example it gives positive and negative numbers in the 1000's. What units does it use or how does it calculate this? Should I be using another application to look at this? Additionally I am running it with a constant NVT setup. ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA ___ 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 simulate a protein and a ATP molecule simultaneity?
Dear GROMACS users:I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer thepdb file to gro file, it said Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms, So how can I build the top file and gro file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity?Best wishes!Mo-Jie Duan ___ 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] g_energy and pressure
Christopher Stiles wrote: I am trying to analyze the pressure of my box with respect to time using g_energy but it seems to give crazy numbers. For example it gives positive and negative numbers in the 1000’s. What units does it use or how does it calculate this? Should I be using another application to look at this? Additionally I am running it with a constant NVT setup. The answer here http://wiki.gromacs.org/index.php/FAQs applies for this question too. 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] how to simulate a protein and a ATP moleculesimultaneity?
Use x2top to build your top file for the ATP, and then used editconf to make the gro file and then u can use genbox to put the protein and the ATP in the same box. Btw I am not 100% on this since I have not done it before but from the vast amounts of reading I have done this seems like what you should do, also take a look at the manual and the wiki to find out how to use these apps. ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, August 08, 2007 9:51 PM To: gmx-users@gromacs.org Subject: [gmx-users] how to simulate a protein and a ATP moleculesimultaneity? Dear GROMACS users: I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer thepdb file to gro file, it said Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms, So how can I build the top file and gro file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity? Best wishes! Mo-Jie Duan ___ 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 simulate a protein and a ATP molecule simultaneity?
[EMAIL PROTECTED] wrote: Dear GROMACS users: I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer the*pdb* file to *gro* file, it said /Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms/, So how can I build the *top* file and *gro* file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity? By reading chapter 5 of the manual thoroughly, understanding how the rtp files work for your force field and modifying your .pdb file and/or force field files to work suitably. 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] Using editconf to center on 0 0 0 , then using genbox
Ok, I don't quite understand something. My dowloaded pdb file of my molecule is centered at about 3 3 3 (in x y z, nm). I perform genbox to solvate it: No problem. I then perform editconf to translate the center of the molecule to 0 0 0 (and move the water likewise): editconf -f Molecule_Solv.gro -o Molecule_Solv -translate -3 -3 -3 [Note here, I'm not using the -center option, b/c I want to place the center of the molecule, not the entire system, at 0 0 0]. No problem here (when I load the structure up in VMD and measure its geometric center, it is indeed at 0 0 0). But then, when I run a simulation on this structure (say a brief energy minimization), it reverts back to its original center at 3 3 3. In other words, the outputted structure after the minimization has the molecule centered back at 3 3 3. Why is this happening??? Does this have anything to do with the dimensions of the box? (which are 6 6 6). The dimensions are irrespective of the centering of the box, right? [I know this seems a little trivial. I'd like to have my molecule centered at 0 0 0, b/c I'll be collecting coordinates later and it'll just make my math easier.] Arneh Babakhani wrote: Hi, I'm using editconf to center my sytem about the origin (0 0 0). No problem there. But then when I use genbox to solvate the resulting structure, the solvent is offset (not centered about 0 0 0). Is there a way to correct this? Have you tried editconf on the solvated structure? Why does it matter anyway? 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 ___ 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] Using editconf to center on 0 0 0 , then using genbox
[I know this seems a little trivial. I'd like to have my molecule centered at 0 0 0, b/c I'll be collecting coordinates later and it'll just make my math easier.] You will have to do that centering after the simulation has been run and the trajectory files written. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] help
In particular, have a look at http://wiki.gromacs.org/index.php/Beginners Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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
