Re: [gmx-users] Simulation of a protein confined in a box
In short - you can apply PBC in all directions (XYZ) by choosing the proper keyword in the .mdp file, I believe the box dimensions are defined in .gro file. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 10, 2008 at 16:00, Lee Soin [EMAIL PROTECTED] wrote: Maybe I didn't put it clearly. My intention is to simulate a protein confined in a box, and the problem is that I don't know how to define a boundary, or a wall, in GROMACS. ___ 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] Simulation of a protein confined in a box
Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. Omer Markovitch wrote: In short - you can apply PBC in all directions (XYZ) by choosing the proper keyword in the .mdp file, I believe the box dimensions are defined in .gro file. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Oct 10, 2008 at 16:00, Lee Soin [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Maybe I didn't put it clearly. My intention is to simulate a protein confined in a box, and the problem is that I don't know how to define a boundary, or a wall, in GROMACS. -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, 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 -- 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
Re: [gmx-users] Simulation of a protein confined in a box
Oh, I didn't read carefully. My suggestion would be, perhaps, to physically put atoms on the sides of the box (possibly, fill each side completely), and to place on them very high repulsion. You might want to freeze them up, and exclude their self interactions from the energy calculation. Good guess Suman. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty [EMAIL PROTECTED]wrote: Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. ___ 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] Opinion: Can position restraining waters increase the speed of the md simulation?
Hi Art, You could, but should you? What do you think to gain? One layer of water is approximately 2.5 A, so with 6 you'd have about two layers of water 'free'. With position restraints on the rest, you'd still be calculating all forces and such, so there's not much gain there. On top of that, the two water layers without position restraints will likely be quite 'icy', giving a severe constriction of your protein dynamics. Basically, your protein dynamics will be close to nonsensical; an undefined and unrealistic restricted ensemble. Now even if you're only interested in the dynamics at an active site, consider that such dynamics is part of the whole-scale protein dynamics. It's not just filling making up most of the protein. Cheers, Tsjerk On Fri, Oct 10, 2008 at 8:25 PM, Arthur Roberts [EMAIL PROTECTED] wrote: Hi, all, In a previous email, I asked about the availability of implicit water calculations in Gromacs 4.0, which might be available in Gromacs 4.1. In the meantime, I was wondering if I position restrained waters that are 6 Angstroms from the protein, would that increase the speed of md simulation, if I have a water shell that extends 15 Angstroms. I would appreciate your input. Best wishes, Art Roberts University of Washington ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [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] Opinion: Can position restraining waters increase the speed of the md simulation?
On a related note, I remember reading a paper recently, where they take a few shells of water molecules with full atomicity, but continuum beyond that. They also took care about the exchange between the molecular water shell and the continuum as the polymer/protein conformation changes during the simulation. I have no idea how computationally efficient that would be though. Regards, Suman. Tsjerk Wassenaar wrote: Hi Art, You could, but should you? What do you think to gain? One layer of water is approximately 2.5 A, so with 6 you'd have about two layers of water 'free'. With position restraints on the rest, you'd still be calculating all forces and such, so there's not much gain there. On top of that, the two water layers without position restraints will likely be quite 'icy', giving a severe constriction of your protein dynamics. Basically, your protein dynamics will be close to nonsensical; an undefined and unrealistic restricted ensemble. Now even if you're only interested in the dynamics at an active site, consider that such dynamics is part of the whole-scale protein dynamics. It's not just filling making up most of the protein. Cheers, Tsjerk On Fri, Oct 10, 2008 at 8:25 PM, Arthur Roberts [EMAIL PROTECTED] wrote: Hi, all, In a previous email, I asked about the availability of implicit water calculations in Gromacs 4.0, which might be available in Gromacs 4.1. In the meantime, I was wondering if I position restrained waters that are 6 Angstroms from the protein, would that increase the speed of md simulation, if I have a water shell that extends 15 Angstroms. I would appreciate your input. Best wishes, Art Roberts University of Washington -- 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
[gmx-users] Re: Protein coming out of the box
Oh...Similar type of problem once I have got, so got reply from some one in archives that if use comm_grps= protein , protein will not come out of the water box.So thats why I have suggested, If I say wrong answer regret for that * Hi, ** Ravi ** Use comm_grps = protein in your .mdp file. ** ** ** 3. protein coming out of the box (ravi sharma) ** * No! You will ruin energy conservation... * ** Hello everyone ** ** my protein coming out of the box in final md how can i fix my ** protein in the middle of the box. can you help me out?? ** * ___ 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] protein coming out of the box
1021 results for protein out box on the gromacs search page (mailing list search). The first so many are relevant. Why not checking the archives first? Oh, and it's mentioned in the wiki too. Tsjerk On Sat, Oct 11, 2008 at 11:03 AM, ravi sharma [EMAIL PROTECTED] wrote: Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? Thanks Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut Bollywood news, movie reviews, film trailers and more! Click here. ___ 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
[gmx-users] Option -shuffle, -sort, -np missing in grompp in version 4.0?
The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? -- Sun Li Department of Physics Nanjing University, China ___ 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] Simulation of a protein confined in a box
This seems to me a very complicated realization. Why doesn't GROMACS provide an easy way for wall simulation? 2008/10/11 Omer Markovitch [EMAIL PROTECTED] Oh, I didn't read carefully. My suggestion would be, perhaps, to physically put atoms on the sides of the box (possibly, fill each side completely), and to place on them very high repulsion. You might want to freeze them up, and exclude their self interactions from the energy calculation. Good guess Suman. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty [EMAIL PROTECTED] wrote: Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. ___ 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 -- Sun Li Department of Physics Nanjing University, China ___ 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:Protein coming out of the box
Hi, Ravi Use comm_grps = protein in your .mdp file. 3. protein coming out of the box (ravi sharma) Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? ___ 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] protein coming out of the box
Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? Thanks Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___ 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: Protein coming out of the box
So how could i do this energy conservation, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On Sat, 11/10/08, sudheer babu [EMAIL PROTECTED] wrote: From: sudheer babu [EMAIL PROTECTED] Subject: [gmx-users] Re: Protein coming out of the box To: gmx-users@gromacs.org Date: Saturday, 11 October, 2008, 4:46 PM Oh...Similar type of problem once I have got, so got reply from some one in archives that if use comm_grps= protein , protein will not come out of the water box.So thats why I have suggested, If I say wrong answer regret for that Hi, Ravi Use comm_grps = protein in your .mdp file. 3. protein coming out of the box (ravi sharma) No! You will ruin energy conservation... Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? ___ 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 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___ 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: Protein coming out of the box
Ravi, Just come to terms with PBC: the box has no outside. Chapter 3 of the manual... Tsjerk On Sat, Oct 11, 2008 at 1:30 PM, ravi sharma [EMAIL PROTECTED] wrote: So how could i do this energy conservation, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On Sat, 11/10/08, sudheer babu [EMAIL PROTECTED] wrote: From: sudheer babu [EMAIL PROTECTED] Subject: [gmx-users] Re: Protein coming out of the box To: gmx-users@gromacs.org Date: Saturday, 11 October, 2008, 4:46 PM Oh...Similar type of problem once I have got, so got reply from some one in archives that if use comm_grps= protein , protein will not come out of the water box.So thats why I have suggested, If I say wrong answer regret for that Hi, Ravi Use comm_grps = protein in your .mdp file. 3. protein coming out of the box (ravi sharma) No! You will ruin energy conservation... Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? ___ 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 Add more friends to your messenger and enjoy! Invite them now. ___ 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] Re:Protein coming out of the box
sudheer babu wrote: Hi, Ravi Use comm_grps = protein in your .mdp file. 3. protein coming out of the box (ravi sharma) No! You will ruin energy conservation... Hello everyone my protein coming out of the box in final md how can i fix my protein in the middle of the box. can you help me out?? ___ 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] Option -shuffle, -sort, -np missing in grompp in version 4.0?
Am Samstag, 11. Oktober 2008 schrieb Lee Soin: The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? These options were used for particle decomposition in the tpr file. Gromacs 4 default method is domain decomposition, but as far as I remember, PD is still optional. The options can be set during run-time so that a tpr input file itself is independent of the parallel setup during runtime (the output may depend upon the runtime environement). Thus you should find all options in mdrun. The -np switch isn't required anymore (for mpi). Please correct me if I'm wrong... Best Martin ___ 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] Simulation of a protein confined in a box
Lee Soin wrote: This seems to me a very complicated realization. Why doesn't GROMACS provide an easy way for wall simulation? How about reading manual section 7.3.20 Walls in the Gromacs-4.0 manual? I think that would be what you're after. -Justin 2008/10/11 Omer Markovitch [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Oh, I didn't read carefully. My suggestion would be, perhaps, to physically put atoms on the sides of the box (possibly, fill each side completely), and to place on them very high repulsion. You might want to freeze them up, and exclude their self interactions from the energy calculation. Good guess Suman. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sun Li Department of Physics Nanjing University, China ___ 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] Option -shuffle, -sort, -np missing in grompp in version 4.0?
Martin Höfling wrote: Am Samstag, 11. Oktober 2008 schrieb Lee Soin: The command grompp used to have options -shuffle, -sort and -np, but it seems that they appear no more with version 4.0? These options were used for particle decomposition in the tpr file. Gromacs 4 default method is domain decomposition, but as far as I remember, PD is still optional. The options can be set during run-time so that a tpr input file itself is independent of the parallel setup during runtime (the output may depend upon the runtime environement). Thus you should find all options in mdrun. The -np switch isn't required anymore (for mpi). Please correct me if I'm wrong... These options have been removed indeed. Domain decomposition is much more efficient than particle decomposition. Therefore PD is useful only in special cases. -- 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] Fatal Error: number of coordinates in coordinate file does not match topology
I want to perform MD Equilibration run under position restrained for 200ps. Bond distances were constrained using the LINCS (Linear Constraints) algorithm, the water molecules were restrained using the SETTLE algorithm. In order to do this I have modified nsteps in original pr.mdp file. Following is the modified file contents: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10 ; total 200 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; 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 Then I wanted to do grompp with this modified pr.mdp file. But it is showing a Fatal error like, Fatal Error: number of coordinates in coordinate file does not match topology. But if I use the original pr.mdp (without modifying it for 200ps) the grompp runs properly. I am not understanding what to do now. Please help me out. Thanking you, Chitrita. ___ 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] Fatal Error: number of coordinates in coordinate file does not match topology
Hi Chitrita, Please copy-paste the exact error and the command line in both cases (working and not working). Also, what platform are you working on? Did you by chance edit the .mdp file under windows? Cheers, Tsjerk On Sat, Oct 11, 2008 at 6:46 PM, Chitrita Dutta Roy [EMAIL PROTECTED] wrote: I want to perform MD Equilibration run under position restrained for 200ps. Bond distances were constrained using the LINCS (Linear Constraints) algorithm, the water molecules were restrained using the SETTLE algorithm. In order to do this I have modified nsteps in original pr.mdp file. Following is the modified file contents: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10 ; total 200 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; 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 Then I wanted to do grompp with this modified pr.mdp file. But it is showing a Fatal error like, Fatal Error: number of coordinates in coordinate file does not match topology. But if I use the original pr.mdp (without modifying it for 200ps) the grompp runs properly. I am not understanding what to do now. Please help me out. Thanking you, Chitrita. ___ 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
[gmx-users] RE: Fatal Error: number of coordinates in coordinate file does not match topology
gurgo I want to perform MD Equilibration run under position restrained for gurgo 200ps. Bond gurgo distances were constrained using the LINCS (Linear Constraints) algorithm, gurgo the water molecules were restrained using the SETTLE algorithm. In order to gurgo do this I have modified nsteps in original pr.mdp file. Following is the gurgo modified file contents: gurgo Then I wanted to do grompp with this modified pr.mdp file. But it is showing gurgo a Fatal error like, gurgo Fatal Error: gurgo number of coordinates in coordinate file does not match topology. gurgo But if I use the original pr.mdp (without modifying it for 200ps) the grompp gurgo runs properly. I am not understanding what to do now. Please help me out. Please tell us all the actions you performed especially the tool you use for modifying .mdp. It seems the problem is in file formats... -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
