Re: [gmx-users] g_rmsf fitting
tangxuan wrote: Hi Tsjerk, Yes, you are right. My protein has multiple subunits. I have a original tpr file ref1.tpr which is the input to start the simulation. I have checked the protein structure in this tpr file. The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. I take out part of the result below and the results are from two methods for same subunit. What happens whan you overlay the two reference structures using g_confrms? Is it high RMSD? Both reference structures and trajectories should be jump-free. -- 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 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] use of distance dependent dielctric
Ran Friedman wrote: It's not implemented AFAIK, but you can use a tabulated function for the Coulomb interactions. That is correct. And what do you mean with distance dependent dielectric? Divide by distance in Ångström? Anyway this is easy to do in a table. Ran. Mark Abraham wrote: [EMAIL PROTECTED] wrote: Hi all, i want to confirm whethere there is a distance dependent dielctric function in GROMACS.I want to use this. Please suggest me the possible sources. You should start by looking in the manual. My guess is that it is not implemented. 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 -- 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 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_rmsf fitting
Hi Tang, The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. So (one of the) subunits occasionally jump(s) back and make the molecule whole. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. Assuming that ref1.tpr corresponds to your starting structure, which has the subunits separated, this means that you end up with a trajectory which has the subunits separated consistently. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. This reference may be of the correct complex (check it). 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. And this will have the subunits separated. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. So the answer is in the structures (jump/nojump) and not in the way g_rmsf performs the fit and calculates the rmsf. Try to make this line of thinking your own and check the structures (references/selected frames from trajectories) first whenever you encounter problems like this. This issue has also been covered before, and I recall having posted a message on this list regarding the correct use of references, fitting and -pbc options using trjconv, which may be useful to you. Cheers, Tsjerk -- 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: gromacs installation (some broken links in wiki?)
Carsten Kutzner wrote: Hi Mahdi, In principle the installation instructions for gromacs should be available here: http://www.gromacs.org/gromacs/installation/installation-instructions.html but for some reason the link does not work. (It seems that the first two links GROMACS and Instructions in the documentation field in the gromacs wiki are broken). OK I bot-crawled the GROMACS wiki and fixed all of these links except those on the main sidebar, for which you need admin privileges. Last I knew, that means David van der Spoel, or Dallas Warren. 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] g_rmsf fitting
Thanks for your detailed explanation. Sorry for my words and I wrote them in a hurry without careful check. In fact, I can not see a whole protein in ref1.tpr and part of subunits are out of box. I do not know if this can be called jump. Tang Tsjerk Wassenaar wrote: Hi Tang, The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. So (one of the) subunits occasionally jump(s) back and make the molecule whole. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. Assuming that ref1.tpr corresponds to your starting structure, which has the subunits separated, this means that you end up with a trajectory which has the subunits separated consistently. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. This reference may be of the correct complex (check it). 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. And this will have the subunits separated. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. So the answer is in the structures (jump/nojump) and not in the way g_rmsf performs the fit and calculates the rmsf. Try to make this line of thinking your own and check the structures (references/selected frames from trajectories) first whenever you encounter problems like this. This issue has also been covered before, and I recall having posted a message on this list regarding the correct use of references, fitting and -pbc options using trjconv, which may be useful to you. Cheers, Tsjerk -- 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 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_rmsf fitting
See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions On Jan 4, 2008 11:20 AM, tangxuan [EMAIL PROTECTED] wrote: Thanks for your detailed explanation. Sorry for my words and I wrote them in a hurry without careful check. In fact, I can not see a whole protein in ref1.tpr and part of subunits are out of box. I do not know if this can be called jump. Tang Tsjerk Wassenaar wrote: Hi Tang, The subunits have no contact each other obviously, without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. However, the structure in the frames shows that there is a whole protein with jump. Therefore, the structure in the tpr file is different from the structure in the first frame. So (one of the) subunits occasionally jump(s) back and make the molecule whole. The simulation is 30ns long and I am trying to calculate the rmsf between 20ns and 30ns. I removed the jumps in whole simulation(trjconv -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc file between 20ns and 30ns. Assuming that ref1.tpr corresponds to your starting structure, which has the subunits separated, this means that you end up with a trajectory which has the subunits separated consistently. The main difference between is the tpr file at 20ns(ref20.tpr) i used and two ways I have used to get it: 1) used ref1.tpr and original trr file to get a tpr file at 20ns ref20.tpr by tpbconv. This reference may be of the correct complex (check it). 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr by tpbconv. And this will have the subunits separated. then g_rmsf -f .xtc (nojump) -s ref20.tpr -res is used to calculate the rmsf. So the answer is in the structures (jump/nojump) and not in the way g_rmsf performs the fit and calculates the rmsf. Try to make this line of thinking your own and check the structures (references/selected frames from trajectories) first whenever you encounter problems like this. This issue has also been covered before, and I recall having posted a message on this list regarding the correct use of references, fitting and -pbc options using trjconv, which may be useful to you. Cheers, Tsjerk -- 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 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] topology treatment in free energy calculations - possible bug
Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? 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/ ___ 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] topology treatment in free energy calculations - possible bug_2nd
Hi once more It just came to my mind, that the behaviour, I described in the first mail will be quite dangerous, whenever #define statements are in the topology, cause this would lead to the insertion of the FF-values in the topology, when preprocessing, and then be copied into the B-state afterwards, even if the values are crap for the B-state... 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/ -- 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/ ___ 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] topology treatment in free energy calculations - possible bug
On Fri, 4 Jan 2008, Maik Goette wrote: Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? it cannot be called as a bug... when you mention parameters for A state in topology explicitly then grompp will expect you to mention the B state parameters also, and if it doesn't find it, it will assign A state parameter to B state. that is quite well documented, i think, in manual. So there is no reason to think it as a bug. bharat Regards -- 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] topology treatment in free energy calculations - possible bug_2nd
Maik, It just came to my mind, that the behaviour, I described in the first mail will be quite dangerous, whenever #define statements are in the topology, cause this would lead to the insertion of the FF-values in the topology, when preprocessing, and then be copied into the B-state afterwards, even if the values are crap for the B-state... As far as treatment of A and B state parameters, I am not sure there is any solution that doesn't result in dangerous behavior in some situations. Therefore my recommendation is that anytime one is handling atoms which are being perturbed (i.e., where the B state *might* be different from the A state) both A and B state parameters be specified explicitly in the topology by the user. David 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/ -- 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/ ___ 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] Question regarding compatibility of UFF and GROMACS
Subhashis Biswas wrote: Hi, I know this issue has been discussed in some form before, but hough may be I resurface it again. Is it possible to transfer a UFF forcefield to a GROMACS forcefield with help of a script? UFF force-field cannot be used in GROMACS as per my understanding, and I renamed the FF types of an UFF based small peptide to GROMACS by hand, but I am afraid this will take for ever in longer systems. Also if someone can highlight upon what is the basic difference in UFF type forcefields and GROMACS (parameter or potential function-wise) that would be great. If *you* can specify which potential forms are used in UFF it is straightforward to determine whether you can use it with GROMACS. As long as it consists of pair potentials for the nonbondeds, it should work fine. Thanks so much for your help. regards, Subhashis Subhashis Biswas Post-doctoral Research Associate Department of Energy, Environment Chemical Engineering Washington University in St Louis 1 Brookings Drive, Mail Stop 1180 St Louis, MO 63130 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] topology treatment in free energy calculations - possible bug
Maik I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 I *think* this behavior is described in the documentation. Basically, anytime A state parameters are specified in the topology and B state are omitted, A state are copied to B state. To make B state different, you have to either (a) specify them explicitly, or (b) have them looked up in the force field where they are different. So this is expected behavior. David Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? 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/ ___ 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] topology treatment in free energy calculations -possible bug
This behavior is itentional. But it can indeed be confusing. Therefore in Gromacs 4.0 a warning will be generated (and I have added a table in the manual that explains all the possible combinations). If you explicitly define parameters for the A-state, I don't see why you would want the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: GMX-mailinglist gmx-users@gromacs.org Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? 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/ ___ 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 _ 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 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] Question regarding compatibility of UFF and GROMACS
Hi, I know this issue has been discussed in some form before, but hough may be I resurface it again. Is it possible to transfer a UFF forcefield to a GROMACS forcefield with help of a script? UFF force- field cannot be used in GROMACS as per my understanding, and I renamed the FF types of an UFF based small peptide to GROMACS by hand, but I am afraid this will take for ever in longer systems. Also if someone can highlight upon what is the basic difference in UFF type forcefields and GROMACS (parameter or potential function- wise) that would be great. Thanks so much for your help. regards, Subhashis Subhashis Biswas Post-doctoral Research Associate Department of Energy, Environment Chemical Engineering Washington University in St Louis 1 Brookings Drive, Mail Stop 1180 St Louis, MO 63130 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question regarding compatibility of UFF and GROMACS
gromacs manual has the answer (FF terms) for you. Subhashis Biswas wrote: Hi, I know this issue has been discussed in some form before, but hough may be I resurface it again. Is it possible to transfer a UFF forcefield to a GROMACS forcefield with help of a script? UFF force-field cannot be used in GROMACS as per my understanding, and I renamed the FF types of an UFF based small peptide to GROMACS by hand, but I am afraid this will take for ever in longer systems. Also if someone can highlight upon what is the basic difference in UFF type forcefields and GROMACS (parameter or potential function-wise) that would be great. Thanks so much for your help. regards, Subhashis Subhashis Biswas Post-doctoral Research Associate Department of Energy, Environment Chemical Engineering Washington University in St Louis 1 Brookings Drive, Mail Stop 1180 St Louis, MO 63130 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww 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] generation of guanidium intramolecular force-field
Thanks for providing the insight about it. I have tried it. I have two query.. (1) As in the case of simulation with urea as a solute and water as solvent the corresponding file urea+h2o.gro file is given there.I have to do simulation similar to urea i.e. guanidium ion as a solute in place of urea.So in that case how will i be able to create Gdm+h2o.gro file analogous to urea+h2o.gro(Gdm=Guanidium ion). (2) If i have to perform simulation with varying concentration of system(Guanidium water), so how will i be able to do it.As i have seen in case of urea+h2o.gro concentration of system is fixed and if i have to generate a system of different molal(different ratio of urea and water), so will be play with concentration. If any help i will be getting, i will be very thankful. kinshuk raj srivastava IIT-Bombay India Quoting [EMAIL PROTECTED]: Hi all, I have been try to put up MD simulation of guanidium chloride simulation in SPC water model.I have been facing problem regarding *.rtp, *.itp file generation for new entry for guanidium ion.If any one is aware about how to create above mentioned file please let me give some insight about file corresponding guanidium ion. I tried to make it with argenine side chain but i have been facing problem while generating above mentioned file. http://wiki.gromacs.org/index.php/Parameterization You could use PRODRG to generate the topology, but you will have to validate the parameters (see the above link), especially the charges that PRODRG assigns. They are often unsatisfactory. -Justin kinshuk raj srivastava IIT-Bombay Mumbai, India ___ 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 [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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] generation of guanidium intramolecular force-field
[EMAIL PROTECTED] wrote: Thanks for providing the insight about it. I have tried it. I have two query.. (1) As in the case of simulation with urea as a solute and water as solvent the corresponding file urea+h2o.gro file is given there.I have to do simulation similar to urea i.e. guanidium ion as a solute in place of urea.So in that case how will i be able to create Gdm+h2o.gro file analogous to urea+h2o.gro(Gdm=Guanidium ion). (2) If i have to perform simulation with varying concentration of system(Guanidium water), so how will i be able to do it.As i have seen in case of urea+h2o.gro concentration of system is fixed and if i have to generate a system of different molal(different ratio of urea and water), so will be play with concentration. If any help i will be getting, i will be very thankful. genconf + genbox kinshuk raj srivastava IIT-Bombay India Quoting [EMAIL PROTECTED]: Hi all, I have been try to put up MD simulation of guanidium chloride simulation in SPC water model.I have been facing problem regarding *.rtp, *.itp file generation for new entry for guanidium ion.If any one is aware about how to create above mentioned file please let me give some insight about file corresponding guanidium ion. I tried to make it with argenine side chain but i have been facing problem while generating above mentioned file. http://wiki.gromacs.org/index.php/Parameterization You could use PRODRG to generate the topology, but you will have to validate the parameters (see the above link), especially the charges that PRODRG assigns. They are often unsatisfactory. -Justin kinshuk raj srivastava IIT-Bombay Mumbai, India ___ 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 [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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. 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 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] generation of guanidium intramolecular force-field
Thanks for providing the insight about it. I have tried it. I have two query.. (1) As in the case of simulation with urea as a solute and water as solvent the corresponding file urea+h2o.gro file is given there.I have to do simulation similar to urea i.e. guanidium ion as a solute in place of urea.So in that case how will i be able to create Gdm+h2o.gro file analogous to urea+h2o.gro(Gdm=Guanidium ion). This is what genbox is for. (2) If i have to perform simulation with varying concentration of system(Guanidium water), so how will i be able to do it.As i have seen in case of urea+h2o.gro concentration of system is fixed and if i have to generate a system of different molal(different ratio of urea and water), so will be play with concentration. Do some back-of-the-envelope calculations about how many solvent molecules you will need for the concentrations you want. It will not be feasible to have more than a few (tens of) thousands of solvent molecules. 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] Gromacs version
Hi, Can anyone please tell me how to find which version of gromacs is installed in a particular system? Since with the path where it is installed, I am unable to make out if it 3.2.1 or 3.3. Thanks in advance, Raghu Forgot the famous last words? Access your message archive online at http://in.messenger.yahoo.com/webmessengerpromo.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
