Re: [gmx-users] can gromacs simulate the c60?
zzhwise1 wrote: hi everyone I am planning to simulated the C60 ,but i am not sure whether the gromacs can simulate it ! I have read a particle that simulated the CNT by using the gromacs and using the Morse potential!so i want to know is it correct to C60?if right,how to get the morse parameters? Probably the best source of information is going to be that paper... Some of these questions you could only answer if you'd done a simulation on C60 already... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] about the position-restrained MD.
Liu Lin wrote: > thanks for your reply! > > but I do not understand. The posre.itp and the .top files are built by > the "pdb2gmx" > they should be matched. Why does it happen that the position restraints > file does not match the topology file .Could you tell me where I can > find the reason. Probably either the posre.itp or .top files have been edited in a manner inconsistent with each other, or you are using files that don't correspond to each other. If all else fails, make a new working directory and repeat your pdb2gmx and/or solvation step to make sure the .top and posre.itp must correspond... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] can gromacs simulate the c60?
hi everyone I am planning to simulated the C60 ,but i am not sure whether the gromacs can simulate it ! I have read a particle that simulated the CNT by using the gromacs and using the Morse potential!so i want to know is it correct to C60?if right,how to get the morse parameters? thanks a lot ! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] about the position-restrained MD.
thanks for your reply! but I do not understand. The posre.itp and the .top files are built by the "pdb2gmx" they should be matched. Why does it happen that the position restraints file does not match the topology file .Could you tell me where I can find the reason. From: Mark Abraham <[EMAIL PROTECTED]>Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] about the position-restrained MD.Date: Fri, 09 Mar 2007 14:21:31 +1100>Liu Lin wrote:> > Dear gmx-users:> >> > I can not finish my position-restrained MD job. When the pr started> > ,it stopped immediately. The log told that> > "Program grompp, VERSION 3.3.1> > Source code file: toppush.c, line: 1108> > Fatal error:> > [ file "posre.itp", line 28 ]:> > Atom index (27) in position_restraints out of bounds (1-25)"> > I can not find out the reason.>>Your job didn't even start the MD... this error message says that grompp>is failing. Your position restraints file doesn't match your topology>somehow, but you'll have to work out why that is so.>>Mark>___>gmx-users mailing listgmx-users@gromacs.org>http://www.gromacs.org/mailman/listinfo/gmx-users>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使用世界上最大的电子邮件系统― MSN Hotmail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] about the position-restrained MD.
Liu Lin wrote: > Dear gmx-users: > > I can not finish my position-restrained MD job. When the pr started > ,it stopped immediately. The log told that > "Program grompp, VERSION 3.3.1 > Source code file: toppush.c, line: 1108 > Fatal error: > [ file "posre.itp", line 28 ]: > Atom index (27) in position_restraints out of bounds (1-25)" > I can not find out the reason. Your job didn't even start the MD... this error message says that grompp is failing. Your position restraints file doesn't match your topology somehow, but you'll have to work out why that is so. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] about the position-restrained MD.
Dear gmx-users: I can not finish my position-restrained MD job. When the pr started ,it stopped immediately. The log told that "Program grompp, VERSION 3.3.1Source code file: toppush.c, line: 1108 Fatal error:[ file "posre.itp", line 28 ]: Atom index (27) in position_restraints out of bounds (1-25)" I can not find out the reason.Please help me. Thanks a lot! Linda使用 MSN Messenger 与联机的朋友进行交流 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 calculate angle dependent rdf
Dear everyone, I read it from the 3.3 manual that the g_rdf program can calculate the angle dependent rdf. But I cannot find how to implement it ? Which option should be chosen or something else? Could anyone help me? Thank you !! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Chimera GROMACS support
All, Just in case there are those on here who don't know, Chimera is a nice viewing program for molecular structures, trajectories, etc. It also has a lot of bells and whistles relating to preparing structures for simulation (i.e. building in missing residues/loops, etc). David On 2/27/07, Eric Pettersen <[EMAIL PROTECTED]> wrote: Hi, The latest snapshot release of UCSF Chimera (versions 1.2348-50) now has explicit support for GROMACS trajectories. It requires .tpr and .trr files as input. If you try it out and run into problems or have suggestions, let me know. The Chimera home page is here: http://www.cgl.ucsf.edu/chimera Follow the "snapshot" link to reach the snapshot section of the download page. The home page also describes the fairly wide variety of features that Chimera has. You can find documentation for just the MD-specific features here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html There's also an MD tutorial here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html though you might want to do the "Getting Started" tutorial first: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html --Eric Eric Pettersen UCSF Computer Graphics Lab [EMAIL PROTECTED] http://www.cgl.ucsf.edu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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] About the evaluation for the free energy of lipid/protein interacion
You might want to start with an introductory simulation book like the one by Andrew Leach. David On 3/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Shulin Zhuang wrote: > Great thanks. Would you like to give me several papers on this field. No, I don't have any, and that's your job :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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: Request
payal kumari wrote: Respected Sir I am working on 1T5A,human pyruvate kinase M2.I mutated the protein at position 391 replacing histidine with tyrosine in chin A.After that performed energy minimization using gromacs..Its showed the warning "Water Box Exploded" what does it mean and how to remove this..please let me know It probably means you have (severe) clashes in your 'mutated' protein structure. This causes atoms to be pushed away with large forces. Try to use a (simple) modeling program (e.g., DeepView/SwissPDBviewer) to resolve the problem. By the way, I do not recall that I have seen this error during energy minimization, it usually shows up only during MD runs (check your mdp settings and mdrun output). -- Groetjes, Anton _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | "This is a Biosheet" (J.G.E.M. Fraaije) | |_|___| ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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: Re: [gmx-users] vacuum right but melt collapse
Hi Kitty, Such a solution is unsatisfactory, as it seems that you're masking an underlying cause. Now, I'm not sure of your other parameters, but when using a cut-off (do you use reaction-field) you would usually (gromos force field) use a twin-range of 0.9/1.4, which is what the force field was parameterized for. If you look at the energies in order to find the cause of a crash, you want to look for the energy term first displaying strange behaviour. You also may want to try setting the neighbour list update to every step. And please, don't use html formatted e-mails... :) Hope it helps, Tsjerk On 3/8/07, kitty ji <[EMAIL PROTECTED]> wrote: Tsjerk Wassenaar, thank you very much for you suggestion even if most of them have been manipulated. "Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, by hand, checking all bonds, angles, dihedrals, exclusion (implicit ones!), etc." when the explosion happened, the energy of bond, angle and potential will were increase. And the topology has been checked several times. Now I increase the cutoff of VDW & Coulomb from 0.9 to 1.5. The system looks ok from last night to this time. If the problem is fixed, I conclude that cutoff 0.9 is not enough for electric system. Hope this conclusion is helpful for GMX users. Message: 2 Date: Wed, 7 Mar 2007 17:49:30 +0100 From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> Subject: Re: Re: [gmx-users] vacuum right but melt collapse To: "kitty ji" <[EMAIL PROTECTED]>, "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=GB2312; format=flowed Hi Ji Qing, Write out the energies at every step and check which of the energy contributions goes astray. This may give you a good clue to where you're mistake is. Also, run through the topology again, by hand, checking all bonds, angles, dihedrals, exclusion (implicit ones!), etc. Good luck, Tsjerk On 3/7/07, kitty ji <[EMAIL PROTECTED]> wrote: > > > Thanks Mark. > But when one polymer chain was used, non-bonded interaction has already been > there. Because one chain means C44H156O22. > After all, I'd like to try more chains. > > Message: 1 > Date: Tue, 06 Mar 2007 17:01:52 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] vacuum right but melt collapse > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=GB2312 > > kitty ji wrote: > > Hi GMX user: > > > > A model for Poly(vinyl methyl ether) was built with OPLS force field ( > > all H ). > > > > > > > > When the model was run alone (a single chain) in vacuum, anything goes ok. > > > > > > > > But with 45 chains box, the system will be collapse with a little bond > > elongates abnormal whatever in NVT or NPT. > > > > > > > > The relax time of pressure and temperature were adjust but no helpful. > > > > > > > > How can I found some possible reason and then fix it ? Any advise will > > be appreciated. > > If an isolated molecule doesn't do anything strange, and two more more > do, then you have a problem with inter-molecular interactions, i.e. the > non-bonded ones. Try with just 2 chains to verify this... and look > carefully at the atom types and the non-bonded parameters for them. > > Mark > > > > * > Ji Qing > Institute of Chemistry, Chinese Academy of Sciences > Tel: 0086-10-62562894 £¬82618423 > * > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 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 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] genbox give coord file more waters than top file
From: "Mark Abraham" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] genbox give coord file more waters than top file Date: Thu, 8 Mar 2007 22:27:01 +1100 (EST) > 8 mar 2007 kl. 01.32 skrev Mark Abraham: > >>> Dear gromacs guys >>> >>> Why would genbox put more water molecules in my .gro file than in >>> my .top >>> file? I'm sure all I have to do is edit the number in my top file, >>> but I >>> have not had this happen before, does anyone know of a reason >>> that this >>> happens so I can fix my file? >> >> genbox doesn't read a top and produce that many solvent molecules. >> For a >> start, how does it know what shape you want them in? Read "man >> genbox", >> choose what you want to do, apply genbox, and then edit your .top >> so the >> number of waters agrees with what genbox produced... not the other way >> around. >> >> Mark >> > > I'm not so sure about that. genbox *does* take a top file as an > optional argument. genbox -h tells me: > > "Finally, genbox will optionally remove lines from your topology file > in which > a number of solvent molecules is already added, and adds a line with the > total number of solvent molecules in your coordinate file." > > I have never used this option, so I don't know exactly how it works, > but I expect it to do what William wants it to do. Maybe this works, I've never used it either... but the point is that the source of the information about how many waters to add comes from the genbox command line, not this .top file. I think William wanted the number of waters in his .top file to be added to his .gro file, and this is an ill-defined proposition. Mark This depends. If the gro and top came out of pdb2gmx, pdb2gmx already recognized the water molecules and wrote the gro and top files. genbox is supposed to regonize these crystal waters in the gro and top file. Normally it would just add a line for the added water molecules. But genbox is so smart that it checks if the waters in the output configuration match the number in the orginal top plus the added waters, and it corrects the top if there is something wrong. I would guess that this is where the error occurs. Please file a bug report to bugzilla.gromacs.org with the gro and top file and the command line used for genbox. Berk. _ FREE pop-up blocking with the new Windows Live Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] genbox give coord file more waters than top file
> 8 mar 2007 kl. 01.32 skrev Mark Abraham: > >>> Dear gromacs guys >>> >>> Why would genbox put more water molecules in my .gro file than in >>> my .top >>> file? I'm sure all I have to do is edit the number in my top file, >>> but I >>> have not had this happen before, does anyone know of a reason >>> that this >>> happens so I can fix my file? >> >> genbox doesn't read a top and produce that many solvent molecules. >> For a >> start, how does it know what shape you want them in? Read "man >> genbox", >> choose what you want to do, apply genbox, and then edit your .top >> so the >> number of waters agrees with what genbox produced... not the other way >> around. >> >> Mark >> > > I'm not so sure about that. genbox *does* take a top file as an > optional argument. genbox -h tells me: > > "Finally, genbox will optionally remove lines from your topology file > in which > a number of solvent molecules is already added, and adds a line with the > total number of solvent molecules in your coordinate file." > > I have never used this option, so I don't know exactly how it works, > but I expect it to do what William wants it to do. Maybe this works, I've never used it either... but the point is that the source of the information about how many waters to add comes from the genbox command line, not this .top file. I think William wanted the number of waters in his .top file to be added to his .gro file, and this is an ill-defined proposition. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] genbox give coord file more waters than top file
From: WILLIAM R WELCH <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] genbox give coord file more waters than top file Date: Wed, 07 Mar 2007 16:53:11 -0600 Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? I have seen this problem for the first time on our Gromacs workshop last week. I think the problem is that genbox does not recognize some crystal waters in your input coordinate file. genbox currently checks for SOL, WAT and HOH. What is the residue name of your crystal waters? The solution for the moment is to manually count the water molecules in the gro file and then correct the top file. Berk. _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] grompp error
Am Donnerstag, 8. März 2007 schrieb best alep: > I got this error everytime, after i change the value, there's still error > message like this but with rcoulomb or rvdw values. Which values did you change? > "ERROR: The cut-off length is longer than half the shortest box vector or > longer than the smallest box diagonal element. Increase the box size or > decrease rlist.Velocities were taken from a Maxwell distribution at 300 K" Did you really increase the boxsize? You need to be a little bit more specific what exactly you did or what you're trying to do. Cheers Martin -- Falls dir die Antwort zu ungenau erscheint, könnte es an der Fragestellung liegen. (Daniel Fass in de.org.ccc) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] PME, epsilon_rf and dielectric constant calculation
Itamar Kass wrote: Dear Mark, I read the manual few times looking for a clue. The only thing I could understand it that epsilon_rf is not taking inti account if I don't use reaction field. Best, Itamar. Mark Abraham wrote: Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? Have you looked in section 7.3? 2. Whet is the best way to calculate the dielectric constant of the simulation box, does g_dipole is enough or should I use g_dielectric also. You need to use g_dipoles -epsilonRF 0 if you have used defaults for PME. If you have used another dielectric for PME (epsilon_surface) then you need to change that in the input to g_dipoles as well. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 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] genbox give coord file more waters than top file
8 mar 2007 kl. 01.32 skrev Mark Abraham: Dear gromacs guys Why would genbox put more water molecules in my .gro file than in my .top file? I'm sure all I have to do is edit the number in my top file, but I have not had this happen before, does anyone know of a reason that this happens so I can fix my file? genbox doesn't read a top and produce that many solvent molecules. For a start, how does it know what shape you want them in? Read "man genbox", choose what you want to do, apply genbox, and then edit your .top so the number of waters agrees with what genbox produced... not the other way around. Mark I'm not so sure about that. genbox *does* take a top file as an optional argument. genbox -h tells me: "Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file." I have never used this option, so I don't know exactly how it works, but I expect it to do what William wants it to do. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] grompp error
Hi, Can anyone help me? I got this error everytime, after i change the value, there's still error message like this but with rcoulomb or rvdw values. "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.Velocities were taken from a Maxwell distribution at 300 K" 8:00? 8:25? 8:40? Find a flick in no time with the Yahoo! Search movie showtime shortcut. http://tools.search.yahoo.com/shortcuts/#news___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] PME, epsilon_rf and dielectric constant calculation
2007/3/8, Itamar Kass <[EMAIL PROTECTED]>: Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? 2. Whet is the best way to calculate the dielectric constant of the simulation box, does g_dipole is enough or should I use g_dielectric also. g_dipole is to calculate the static dielectric constant, g_dielectric is to calculate the frenquency-dependent dielectric constant. Best, Itamar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Sincerely yours, ** Baofu Qiao, PhD Frankfurt Institute for Advanced Studies Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
