[gmx-users] water medium
dear friends i want to simulate a water medium in which 5 types of different ions flow in it. how can i do that with gromacs? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RMSIP (Root mean square inner products)?
Please tell me how gromacs calculates degree of overlap between conformational spaces of the two proteins is it from RMSIP (Root mean square inner products)? if yes then give me the reference in gromacs tutorial 4.0 -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] very low speed in simulation !( need for help)
Dear gmx-usres, In our university we have a cluster containing 20 nodes each with 4 processors, which I want to use that for the simulation project. As a test I submitted a run that I have tested it before in the Imperial College (London). Here the structure of the cluster is so that I should specify on which nodes I want the simulation to be done. for this we have a folder (gromacs launcher), in which there are some files. in the file (lamhosts.txt) the node numbers that I can have access to them, have been specified by the head of cluster. And in the file (hosts.txt) I can choose the nodes which I want to simulate my system with them, (I am resricted to use only the nodes that are listes in the lamhosts.txt). whan I want to use the grompp order, it wants me to specify the -np option(number of processors). For example I can have access to 12 processors (or 3 nodes). I write these commands: /usr/local/gromacs/bin/grompp -c ~.gro -f ~.mdp -p ~.top -n ~.ndx -o topol.tpr -np 12 mpiexec /usr/local/gromacs/bin/mdrun -v -s topol.tpr -np 12 I receive the error that I should include the server name in the list of nodes . I did it for both the lamhosts.txt and hosts.txt file. Then I should write number of processors 13 instead of 12. In this way the simulation goes very very slowly, as I see that if I run the simulation on one processor the speed is more satisfying !!!. I think this low speed is because of including the server in the processor list, and because the server is always busy with other jobs, the speed falls down. Now: 1) Is the reason for low speed , including the server in the list? 2) is the way that let me not to include the server in the list of lamhosts.txt and hosts.txt? It would be greatly appreciated if you guide me as I am completely confused !!! thanks in advance. D. M -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] DSSP
Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] very low speed in simulation !( need for help)
Hi, On May 18, 2010, at 9:35 AM, delara aghaie wrote: Dear gmx-usres, In our university we have a cluster containing 20 nodes each with 4 processors, which I want to use that for the simulation project. As a test I submitted a run that I have tested it before in the Imperial College (London). Here the structure of the cluster is so that I should specify on which nodes I want the simulation to be done. for this we have a folder (gromacs launcher), in which there are some files. in the file (lamhosts.txt) the node numbers that I can have access to them, have been specified by the head of cluster. And in the file (hosts.txt) I can choose the nodes which I want to simulate my system with them, (I am resricted to use only the nodes that are listes in the lamhosts.txt). whan I want to use the grompp order, it wants me to specify the -np option(number of processors). For example I can have access to 12 processors (or 3 nodes). I write these commands: /usr/local/gromacs/bin/grompp -c ~.gro -f ~.mdp -p ~.top -n ~.ndx -o topol.tpr -np 12 mpiexec /usr/local/gromacs/bin/mdrun -v -s topol.tpr -np 12 I think the -np 12 should go directly after the mpiexec. I receive the error that I should include the server name in the list of nodes . I did it for both the lamhosts.txt and hosts.txt file. If you are using LAM MPI, you have to set up the parallel environment with the command lamboot before you start any parallel job with mpirun or mpiexec. LAM requires that the node you run lamboot on is in the list of hosts. This is what the error message says. You can boot a parallel environment with more nodes than you actually use for your parallel job, and I think there is probably a way to tell lam which of the lambooted nodes it should then use for the run. (i.e. all but the server in your case). The other solution would be to log in to one of the nodes which is in the hosts file and issue the lamboot and the mpirun/mpiexec commands there. For better scalability you might also want to upgrade to Gromacs 4. Carsten Then I should write number of processors 13 instead of 12. In this way the simulation goes very very slowly, as I see that if I run the simulation on one processor the speed is more satisfying !!!. I think this low speed is because of including the server in the processor list, and because the server is always busy with other jobs, the speed falls down. Now: 1) Is the reason for low speed , including the server in the list? 2) is the way that let me not to include the server in the list of lamhosts.txt and hosts.txt? It would be greatly appreciated if you guide me as I am completely confused !!! thanks in advance. D. M -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: minimizing ligand only
Dear Justin, thank you for your answer. Actually I did the changes that you suggest, but the problem seems to be the fact that I called lig my molecule. In fact, the error message told that The moleculetype lig is redefined. When I changed its name, it seemed to work. Is there some problem in GROMACS if I use lig to name a molecule? Another question: if I start directly from the ligand, I cannot start the minimization, I am forced to start from editconf to create an empty box because GROMACS complains that the values for cut-off are larger than box dimensions. So, to minimize a molecule, do I have at least to insert it into a box, even if I don't want to add water? It's not a problem for me to do it, it's only to know what is the proper procedure to minimize in vacuo a small ligand. Thanks again and regards Anna Message: 3 Date: Mon, 17 May 2010 12:30:17 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] minimizing ligand only To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf16f19.5000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it does not recognize the moleculetype. The command I used was: grompp -f em.mdp -c lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top I made two attempts: first, I used the .itp file directly coming from PRODRG, second, I modified this file by adding the missing infos on my ligand under the different parts [ molecules ], [ systems] and so on. But I was not able to force Gromacs recognizing my molecule. Obviously, my ligand is not a peptide, but is a small molecule. I searched for some hints in the gmx-users archive and found this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html but it seems to me that it does not answer to my problem. If I follow the Kerrigan's tutorial, it indicates how to create a topology for the ligand, but not how to minimize it in the absence of the protein. Could you give me a more clear explanation? Sorry if the request seems to be trivial, but I really can't understand what to do. You just need to create a proper .top file from the .itp file. There is very little to do in order to make this change: http://www.gromacs.org/Documentation/File_Formats/.itp_File If you need further help, please post the actual error message and your topology. On a separate note, if you're using an unedited PRODRG topology, the charges and charge groups (at face value) are often unsatisfactory, so do proceed carefully... -Justin Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it mailto:amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you're too small to make a change, try sleeping with a mosquito -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: OPLS-AA/L force field
Hi You Zou, Complementing Justin's message, I would invite you to take a look at acpype.googlecode.com. It's my attempt to address problems like yours. There's also links to some options besides ACPYPE. Bear in mind that you should know what you're doing. I would suggest you to read the Wiki's there as well as several references also indicated there. ACPYPE is far from being perfect but it can be very helpful. I have my own methodology where it would require using RED Server for accurate partial charge calculations (ACPYPE may use SQM, which is semi-empirical, via Antechamber), then ACPYPE (which is mostly designed for Amber FF) and then MKTOP for getting the oplsaa atom types. Feel free to contact. Best regards, Alan On Tue, May 18, 2010 at 01:28, gmx-users-requ...@gromacs.org wrote: Message: 2 Date: Mon, 17 May 2010 12:58:09 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] OPLS-AA/L force field To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf175a1.9040...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not? No. You can't use two different force fields in one simulation system. If I can't use this server, how can I make .gro file and .itp file for drug that remove from initial .pdb file? There are several programs in the User Contributions from the website, x2top (which is distributed with Gromacs), or you can build the topology by hand. No matter what you choose, you need a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Selecting groups for analysis in batch submission
Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: minimizing ligand only
To the second question: PRODRG makes usually a very small box (sometimes smaller then the molecule, if i remember correctly), so if you want to use periodic boundary conditions you must make the box large enough, so that there are no problems with cut-offs. The easiest way to make the minimisation in vaccuo would be that you set 'pbc=no' (then you have no problems with the box size). I think with 'pbc=no' you will also need 'ns_type=simple'. Then since you will have only few particals you can also disable the cut-offs entirely (set them all to zero). Greetings Thomas Message: 1 Date: Tue, 18 May 2010 10:28:32 +0200 From: Anna Marabotti anna.marabo...@isa.cnr.it Subject: [gmx-users] Re: minimizing ligand only To: gmx-users@gromacs.org Message-ID: 9609d6a92b3d4297941ed608b4e26...@annanetbook Content-Type: text/plain; charset=us-ascii Dear Justin, thank you for your answer. Actually I did the changes that you suggest, but the problem seems to be the fact that I called lig my molecule. In fact, the error message told that The moleculetype lig is redefined. When I changed its name, it seemed to work. Is there some problem in GROMACS if I use lig to name a molecule? Another question: if I start directly from the ligand, I cannot start the minimization, I am forced to start from editconf to create an empty box because GROMACS complains that the values for cut-off are larger than box dimensions. So, to minimize a molecule, do I have at least to insert it into a box, even if I don't want to add water? It's not a problem for me to do it, it's only to know what is the proper procedure to minimize in vacuo a small ligand. Thanks again and regards Anna Message: 3 Date: Mon, 17 May 2010 12:30:17 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] minimizing ligand only To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf16f19.5000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it does not recognize the moleculetype. The command I used was: grompp -f em.mdp -c lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top I made two attempts: first, I used the .itp file directly coming from PRODRG, second, I modified this file by adding the missing infos on my ligand under the different parts [ molecules ], [ systems] and so on. But I was not able to force Gromacs recognizing my molecule. Obviously, my ligand is not a peptide, but is a small molecule. I searched for some hints in the gmx-users archive and found this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html but it seems to me that it does not answer to my problem. If I follow the Kerrigan's tutorial, it indicates how to create a topology for the ligand, but not how to minimize it in the absence of the protein. Could you give me a more clear explanation? Sorry if the request seems to be trivial, but I really can't understand what to do. You just need to create a proper .top file from the .itp file. There is very little to do in order to make this change: http://www.gromacs.org/Documentation/File_Formats/.itp_File If you need further help, please post the actual error message and your topology. On a separate note, if you're using an unedited PRODRG topology, the charges and charge groups (at face value) are often unsatisfactory, so do proceed carefully... -Justin Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it mailto:amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you're too small to make a change, try sleeping with a mosquito -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] crystallographic water to tip4p model
Hi, I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set -water tip4p it protonates oxygens to spc water model instead. Is there any way to replace spc water molecules with tip4p water molecules in the same orientation? Btw what happen if I'll keep 2 types of water models in one simulation? thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Selecting groups for analysis in batch submission
Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selecting groups for analysis in batch submission
Anirban Ghosh wrote: Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] water medium
tahereh tekieh wrote: dear friends i want to simulate a water medium in which 5 types of different ions flow in it. how can i do that with gromacs? thanks Assuming they are monoatomic, you can use genion after you have added water. If they are polyatomic, use genbox -ci -nmol (before filling the box with water). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: minimizing ligand only
Anna Marabotti wrote: Dear Justin, thank you for your answer. Actually I did the changes that you suggest, but the problem seems to be the fact that I called lig my molecule. In fact, the error message told that The moleculetype lig is redefined. When I changed its name, it seemed to work. Is there some problem in GROMACS if I use lig to name a molecule? The error suggests you have two [moleculetype] directives for lig thus repeating its definition. Another question: if I start directly from the ligand, I cannot start the minimization, I am forced to start from editconf to create an empty box because GROMACS complains that the values for cut-off are larger than box dimensions. So, to minimize a molecule, do I have at least to insert it into a box, even if I don't want to add water? It's not a problem for me to do it, it's only to know what is the proper procedure to minimize in vacuo a small ligand. You always need to define a proper unit cell for conducting a simulation. -Justin Thanks again and regards Anna Message: 3 Date: Mon, 17 May 2010 12:30:17 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] minimizing ligand only To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf16f19.5000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it does not recognize the moleculetype. The command I used was: grompp -f em.mdp -c lig.pdb -o ligmin.tpr -o ligtopol_by_PRODRG.top I made two attempts: first, I used the .itp file directly coming from PRODRG, second, I modified this file by adding the missing infos on my ligand under the different parts [ molecules ], [ systems] and so on. But I was not able to force Gromacs recognizing my molecule. Obviously, my ligand is not a peptide, but is a small molecule. I searched for some hints in the gmx-users archive and found this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037164.html but it seems to me that it does not answer to my problem. If I follow the Kerrigan's tutorial, it indicates how to create a topology for the ligand, but not how to minimize it in the absence of the protein. Could you give me a more clear explanation? Sorry if the request seems to be trivial, but I really can't understand what to do. You just need to create a proper .top file from the .itp file. There is very little to do in order to make this change: http://www.gromacs.org/Documentation/File_Formats/.itp_File If you need further help, please post the actual error message and your topology. On a separate note, if you're using an unedited PRODRG topology, the charges and charge groups (at face value) are often unsatisfactory, so do proceed carefully... -Justin Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it mailto:amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you're too small to make a change, try sleeping with a mosquito -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selecting groups for analysis in batch submission
Thanks a lot Justin. On Tue, May 18, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to calculate the distance between a number of atom pairs using g_dist. For this I want to submit the job through a submission script so that g_dist calculates the distances for all the pairs one after the other. But I need to select the two groups from an index file. How can I give this selection of groups in the script, instead of interactively? Any suggestion is welcome. http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PLUMED release 1.2.0 available
The PLUMED Developers are proud to announce that the NEW version of PLUMED, version number 1.2.0, is available from http://merlino.mi.infn.it/plumed PLUMED is a plugin for free-energy calculations in molecular systems that can be interfaced with some of the most popular molecular dynamics codes using a simple patching procedure. PLUMED allows one to perform several type of calculations, including: - Metadynamics with a wide variety of order parameters - Combined parallel tempering and metadynamics - Bias-exchange metadynamics - Umbrella sampling - Steered MD In this NEW release: * Compatibility with the parallel implementation of SANDER * Adiabatic Biased Molecular Dynamics * Redesigned Multiple Walkers * Inversion condition for the treatment of CV boundaries * External fixed potential acting on CVs * Read and write metadynamics bias from/to file * Steerplan for complex steered MD simulations * Add a constant force on CVs * New standalone utility to run PLUMED as an external tool * New format for COLVAR file with tags * New CVs: potential energy, similarity to alpha helix and beta sheet structure, distance from and projection onto a generic axis, difference between distances * Added support for LAMMPS, Quantum-ESPRESSO, NAMD 2.7b2 and GROMACS 4.0.7 We are also pleased to announce that a Cecam tutorial about PLUMED will take place in Lausanne (Switzerland) from September 28 to October 1, 2010. The deadline for applications is May 31, 2010. For further information and to see a preliminary program, visit sites.google.com/site/plumedtutorial2010 The PLUMED Developers Team-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] DSSP
Shahid, Before trying for do_dssp a gromacs utility calling dssp program , try first dssp program itself by passing simple input like pdb and I hope by that way you can resolve your problem B.Nataraj -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]on Behalf Of shahid nayeem Sent: Tuesday, May 18, 2010 5:17 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] DSSP Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at] vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Need Help about GROMACS.
Archana S Achalere wrote: Thank you Dr. Justin for the reply. Here are the details of my simulation. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I am using 128 DPPC and 3655 water. The .pdb file is taken from Prof. Tieleman's page, University of Calgary. I am trying to calculate water flux across the bilayer. I apply the force by using nonequilibrium MD simulation option in .mdp file, where the acceleration on two groups DPPC and water is given such that the total force on each group would be equal and opposite. I face two problems: 1. If I remove center of mass motion of whole System then the simulation box starts suppressing along z direction (bilayer normal) and eventually simulation terminates after few thousands of time steps. Well, you face a tenuous position. You are forcing two groups together, and unless they are delicately balanced, you'll wind up just crashing the whole thing anyway. 2. If I give two groups DPPC and water for center of mass motion removal, then bilayer moves along z direction (bilayer normal). I would think that this is the correct method for COM motion removal, but what you're seeing suggests there is a net force on the system (see below). snip ; Non-equilibrium MD stuff acc-grps = DPPC SOL accelerate = 0.0 0.0 0.07 0.0 0.0 -0.1 Using these accelerations, you have a slight imbalance in your forces. Using some crude and quick calculations: DPPC = 734 amu, water = 18 amu 734*128 = 90282 18*3655 = 65790 90282*0.07 = 6319.74 65790*0.1 = 6579 The two resulting forces should be equal in magnitude, but as you can see, they are not. The force applied by the water exceeds that applied by DPPC, so you see the net motion along the z-axis. -Justin freezegrps = freezedim= cos-acceleration = 0 deform = -Regards, Archana. On Mon, 17 May 2010, Justin A. Lemkul wrote: Regardless of whether or not you've received a response, please keep all correspondence on the gmx-users list. I am not a private tutor. To what post are you referring? The list is fairly high-traffic, so if it's been a long time since you posted, don't continue to wait for a response. Post a new question, expanding upon your previous problem with any new details. You're more likely to get help if you demonstrate you are trying to help yourself. You're applying opposing forces between your lipids and water? That certainly sounds like a recipe for collapse. Perhaps if you can describe (by posting to the list) what you're doing, what you're hoping to accomplish, and what your .mdp settings are, you might get some more useful advice. -Justin Archana S Achalere wrote: Dear Dr. Justin Lamkul, I apologies that I am writing directly to you the query about my simulation. As since long I have not got any response of my query posted on gmx-users. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I face two problems: 1. If I remove center of mass motion of whole System then the simulation box stars suppressing along z direction (bilayer normal) and eventually simulation terminates after few thousands of time steps. 2. If I give two groups DPPC and water for center of mass motion removal, then bilayer moves along z direction (bilayer normal). Could you please give me some direction how to resolve this. Thank you. Regards, -Archana Department of Chemical Engineering, Indian Institute of Science, Bangalore, India. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulated annealing (SA)
Hi gromacs users 1) after doing simulated annealing simulation, who can I understand that obtained structure is in global minimum and not in local minimum? 2) who can I understand that parameters used in mdp file (annealing_npoints, annealing_time, annealing_temp) are true? Any help will highly appereciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DSSP
shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file What is your exact command line? -Justin Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[gmx-users] PCA
I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows: 1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix? 2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened the eigenval.xvg file it will shows nothing, i don't know what was wrong with it? 3. what is the difference between covariance matrix and normal mode analysis because both were used to generate the eigenval.xvg and eigenvec.trr file? 4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the structures generated at the time of simulations of single structure without using the other structure? I mean to say that it is possible to use single structure as initial to simulate and ED sampling? 5. what is the need of eigenvec2.trr input file in g_anaeig to generate the single number of covariance matrix as shown in manual? I have used to input only one eigenvec.trr and eigenval.xvg, then it is right to do this? 6. I have used eigenval.xvg as input file in g_anaeig which do not shows nothing when used to open in xmgrace. Then how this file used for generating eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have were successfully generated). 7. One last question is related to g_analyze that it reads ascii file and analyze data sets, but in actual it used some graph.xvg file as input. I am confused about this graph.xvg file which file should I used for input to calculate the cosine content of the principal components. -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Need Help about GROMACS.
I think the force I have applied on the two systems balance each other. If I calculate total force on each group: DPPC = 734 amu, water = 18 amu 734*128 = 93952 (This thing you calculated as 90282) 18*3655 = 65790 93952*0.07 = 6576.64 65790*0.1 = 6579 If I reduce values of acceleration by one order of magnitude: ; Non-equilibrium MD stuff acc-grps = DPPC SOL accelerate = 0.0 0.0 0.007 0.0 0.0 -0.01 and remove the center of mass motion of DPPC and water the simulation works well. In this case bilayer do not move along Z direction. But very few water can cross. So I am interested to give higher force so that I can observe large amount of water crossing the bilayer. Which I do see but then bilayer keeps moving along bilayer normal. -archana. On Tue, 18 May 2010, gmx-users-requ...@gromacs.org wrote: Message: 1 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Need Help about GROMACS. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf28b9c.9040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Archana S Achalere wrote: Thank you Dr. Justin for the reply. Here are the details of my simulation. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I am using 128 DPPC and 3655 water. The .pdb file is taken from Prof. Tieleman's page, University of Calgary. I am trying to calculate water flux across the bilayer. I apply the force by using nonequilibrium MD simulation option in .mdp file, where the acceleration on two groups DPPC and water is given such that the total force on each group would be equal and opposite. I face two problems: 1. If I remove center of mass motion of whole System then the simulation box starts suppressing along z direction (bilayer normal) and eventually simulation terminates after few thousands of time steps. Well, you face a tenuous position. You are forcing two groups together, and unless they are delicately balanced, you'll wind up just crashing the whole thing anyway. 2. If I give two groups DPPC and water for center of mass motion removal, then bilayer moves along z direction (bilayer normal). I would think that this is the correct method for COM motion removal, but what you're seeing suggests there is a net force on the system (see below). snip ; Non-equilibrium MD stuff acc-grps = DPPC SOL accelerate = 0.0 0.0 0.07 0.0 0.0 -0.1 Using these accelerations, you have a slight imbalance in your forces. Using some crude and quick calculations: DPPC = 734 amu, water = 18 amu 734*128 = 90282 18*3655 = 65790 90282*0.07 = 6319.74 65790*0.1 = 6579 The two resulting forces should be equal in magnitude, but as you can see, they are not. The force applied by the water exceeds that applied by DPPC, so you see the net motion along the z-axis. -Justin freezegrps = freezedim= cos-acceleration = 0 deform = -Regards, Archana. On Mon, 17 May 2010, Justin A. Lemkul wrote: Regardless of whether or not you've received a response, please keep all correspondence on the gmx-users list. I am not a private tutor. To what post are you referring? The list is fairly high-traffic, so if it's been a long time since you posted, don't continue to wait for a response. Post a new question, expanding upon your previous problem with any new details. You're more likely to get help if you demonstrate you are trying to help yourself. You're applying opposing forces between your lipids and water? That certainly sounds like a recipe for collapse. Perhaps if you can describe (by posting to the list) what you're doing, what you're hoping to accomplish, and what your .mdp settings are, you might get some more useful advice. -Justin Archana S Achalere wrote: Dear Dr. Justin Lamkul, I apologies that I am writing directly to you the query about my simulation. As since long I have not got any response of my query posted on gmx-users. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I face two problems: 1. If I remove center of mass motion of whole System then the simulation box stars suppressing along z direction (bilayer normal) and eventually simulation terminates after few thousands of time steps. 2. If I give two groups DPPC and water for center of mass motion removal, then bilayer moves along z direction (bilayer normal). Could you please give me some direction how to resolve this. Thank you. Regards, -Archana Department of Chemical Engineering, Indian Institute of Science, Bangalore, India. -- 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
Re: [gmx-users] Re: Need Help about GROMACS.
Archana S Achalere wrote: I think the force I have applied on the two systems balance each other. If I calculate total force on each group: DPPC = 734 amu, water = 18 amu 734*128 = 93952 (This thing you calculated as 90282) Ah yes, typo. Sorry :) 18*3655 = 65790 93952*0.07 = 6576.64 65790*0.1 = 6579 If I reduce values of acceleration by one order of magnitude: ; Non-equilibrium MD stuff acc-grps = DPPC SOL accelerate = 0.0 0.0 0.007 0.0 0.0 -0.01 and remove the center of mass motion of DPPC and water the simulation works well. In this case bilayer do not move along Z direction. But very few water can cross. So I am interested to give higher force so that I can observe large amount of water crossing the bilayer. Which I do see but then bilayer keeps moving along bilayer normal. Well, you technically still have a force imbalance, which you can modify by the values of the acceleration. As I pointed out before, you're looking to do something very delicate. If you increase the magnitude of the acceleration, you increase the magnitude of the imbalance, thus you have a net force and a system that has elements colliding within it. This is a potentially very unstable setup. At the very least, balance the forces as best you can (-0.1 z-acceleration for SOL, 0.70025 for DPPC, or some other combination that works out exactly). -archana. On Tue, 18 May 2010, gmx-users-requ...@gromacs.org wrote: Message: 1 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: Need Help about GROMACS. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf28b9c.9040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Archana S Achalere wrote: Thank you Dr. Justin for the reply. Here are the details of my simulation. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I am using 128 DPPC and 3655 water. The .pdb file is taken from Prof. Tieleman's page, University of Calgary. I am trying to calculate water flux across the bilayer. I apply the force by using nonequilibrium MD simulation option in .mdp file, where the acceleration on two groups DPPC and water is given such that the total force on each group would be equal and opposite. I face two problems: 1. If I remove center of mass motion of whole System then the simulation box starts suppressing along z direction (bilayer normal) and eventually simulation terminates after few thousands of time steps. Well, you face a tenuous position. You are forcing two groups together, and unless they are delicately balanced, you'll wind up just crashing the whole thing anyway. 2. If I give two groups DPPC and water for center of mass motion removal, then bilayer moves along z direction (bilayer normal). I would think that this is the correct method for COM motion removal, but what you're seeing suggests there is a net force on the system (see below). snip ; Non-equilibrium MD stuff acc-grps = DPPC SOL accelerate = 0.0 0.0 0.07 0.0 0.0 -0.1 Using these accelerations, you have a slight imbalance in your forces. Using some crude and quick calculations: DPPC = 734 amu, water = 18 amu 734*128 = 90282 18*3655 = 65790 90282*0.07 = 6319.74 65790*0.1 = 6579 The two resulting forces should be equal in magnitude, but as you can see, they are not. The force applied by the water exceeds that applied by DPPC, so you see the net motion along the z-axis. -Justin freezegrps = freezedim= cos-acceleration = 0 deform = -Regards, Archana. On Mon, 17 May 2010, Justin A. Lemkul wrote: Regardless of whether or not you've received a response, please keep all correspondence on the gmx-users list. I am not a private tutor. To what post are you referring? The list is fairly high-traffic, so if it's been a long time since you posted, don't continue to wait for a response. Post a new question, expanding upon your previous problem with any new details. You're more likely to get help if you demonstrate you are trying to help yourself. You're applying opposing forces between your lipids and water? That certainly sounds like a recipe for collapse. Perhaps if you can describe (by posting to the list) what you're doing, what you're hoping to accomplish, and what your .mdp settings are, you might get some more useful advice. -Justin Archana S Achalere wrote: Dear Dr. Justin Lamkul, I apologies that I am writing directly to you the query about my simulation. As since long I have not got any response of my query posted on gmx-users. I am simulating lipid bilayer (DPPC + water) where I give equal and opposite force (along bilayer normal) on lipid and water molecules I face two problems: 1. If I remove center of mass motion of whole System then the simulation
[gmx-users] making index file
Hi, could you guide me how one can create .ndx file format. I thought it would be accessible in library directory like rtp ..files. Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] making index file
Moeed skrev: Hi, could you guide me how one can create .ndx file format. I thought it would be accessible in library directory like rtp ..files. Thanks, Use make_ndx to create a ndx file. The format is pretty straightforward and the files themselves quite readable. Not enoyable, mind you, but readable. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Computational Alanine Scanning
When you re-generate hydrogens, you are introducing some extra disorder to the system. What I did is to write a script to rename the hydrogens. For example, there are residues that have the hydrogen numbering starting from 2 (eg. hydrogens on CB of lysine had hydrogens starting from HB2). In the script I renamed the hydrogens to start on number 1. Also I had to rename ILE atoms (C|H)D1? to (C|H)D?, where (C|H) stands for carbon or hydrogen and ? stands for any character. Also I had to rename atoms in the N and C terminus. When you have doubt in the atom naming, you can see in the RTP file. After doing that, so I didn't have to re-generate hydrogen, I got a smooth energy graph in the EM, that I didn't get by re-generating the hydrogens. Re-generating hydrogens and also re-generating atomic velocities introduce disorder to your system. Best regards. Lucio Montero. Laboratorio del Dr. Federico Sánchez Ext. 27666 Departamento de Biología Molecular de Plantas Instituto de Biotecnología, UNAM Cuernavaca, Morelos, 62210 El mar, 18-05-2010 a las 14:22 +1000, Mark Abraham escribió: - Original Message - From: Binh Khanh Mai khanhbinh...@yahoo.com Date: Tuesday, May 18, 2010 14:10 Subject: [gmx-users] Computational Alanine Scanning To: gmx-users@gromacs.org --- | Dear all, I'm trying use GROMACS to calculate binding free energy with MM-PBSA method and do Computational Alanine Scanning. After run MD and obtain pdb files, I use PYMOL to mutate one residue to Alanine to estimate the energy difference between 2 structures. My issue is that I don't know how to generate topology file (.top file) after mutation but not ignore hydrogen in initial file. If using pdb2gmx command, it needs me ignore hydrogen and I think hydrogen after using this command is not in the same place with hydrogen at first. This will my my results unbelievable. Do your mutation with PYMOL, and later plan to use those coordinates as inputs to grompp. Use pdb2gmx however you need to in order to create the new .top. Assuming PYMOL is not messing around with atom/residue naming and ordering except for the mutated residue, all you have to do is edit a copy of the PYMOL coordinate file so that the new residue has atom names, residue names and atom ordering that match the .top. Then supply the .top with the fixed coordinate file to grompp. Alternatively, work out why pdb2gmx requires you to ignore and regenerate hydrogens, and fix the issue there. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RMSIP (Root mean square inner products)?
- Original Message - From: pawan raghav pwnr...@gmail.com Date: Tuesday, May 18, 2010 17:34 Subject: [gmx-users] RMSIP (Root mean square inner products)? To: gmx-users@gromacs.org Please tell me how gromacs calculates degree of overlap between conformational spaces of the two proteins is it from RMSIP (Root mean square inner products)? if yes then give me the reference in gromacs tutorial 4.0 GROMACS probably doesn't have a shrink-wrapped tool to calculate this. You can probably get the job done with some combination of tools, however. IIRC someone asked about this previously on the list, so please search. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] crystallographic water to tip4p model
- Original Message - From: Павел Кудрявцев pavk...@gmail.com Date: Tuesday, May 18, 2010 20:55 Subject: [gmx-users] crystallographic water to tip4p model To: gmx-users@gromacs.org Hi, I wanna keep crystallographic water with tip4p model for md simulation but when I use pdb2gmx even if I set -water tip4p it protonates oxygens to spc water model instead. Is there any way to replace spc water molecules with tip4p water molecules in the same orientation? What's your GROMACS version and command line? Btw what happen if I'll keep 2 types of water models in one simulation? Your reviewers will giggle. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulated annealing (SA)
- Original Message - From: shahab shariati shahab.shari...@gmail.com Date: Tuesday, May 18, 2010 23:36 Subject: [gmx-users] simulated annealing (SA) To: gmx-users@gromacs.org Hi gromacs users 1) after doing simulated annealing simulation, who can I understand that obtained structure is in global minimum and not in local minimum? Nobody can tell that. The only magic property of the global minimum is that it's lower than all the others. So if you can find all basins... 2) who can I understand that parameters used in mdp file (annealing_npoints, annealing_time, annealing_temp) are true? There's no One True Way. Have a read of relevant literature, see what they do, and if you like their results, do something comparable and sensible. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: gmx-users Digest, Vol 73, Issue 109
Dear Friends I tried to obtain the XY density maps of the heme using g_densmap tool. The molecule was centered in the box The system was rotated to maintain the XY plane on the molecular plane. In the reference gro file, the molecule was also centered and the plane XY was on the molecular plane. To create the reference gro file editconf_mpi_d -f heme.gro -c -o heme_centered.gro -n index.ndx -princ To center the molecule in the box trjconv_mpi_d -f md10ns_heme.xtc -o md10ns_heme_centered.xtc -n index.ndx -s dmpr.tpr -center -boxcenter rect -pbc atom Rotations and translations were eliminated and the XY axis on the XY molecular plane trjconv_mpi_d -f md10ns_heme_centered.xtc -o md10ns_heme_centrado_centered_rottrans.xtc -n index.ndx -s heme_centered.gro -fit rot+trans To obtain the XY density map g_densmap_d -f md10ns_heme_centrado_centered_rottrans.xtc -s heme_centered.gro -n index.ndx -o densmap.xpm The result show the molecule in the corner of the figure and a diffuse withe region around the molecule. I will expect a more defined region around the molecule and centered. I need help, thanks Regards Ricardo _ Gagnez 10 000 $ avec Hotmail! Participez ici. http://go.microsoft.com/?linkid=9729718-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to define an index file
Hello, I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system. To do this how should I define my index groups. Should I include all 125 molecuels in index file? now I have only the first 20 atoms (first molecule).. make_ndx -f Hexane-0.25nm3-index.gro -o index.ndx Reading structure file --- Program make_ndx, VERSION 4.0.7 Source code file: gmx_fatal.c, line: 511 Fatal error: Unexpected end of file in file Hexane-0.25nm3-index.gro at line 2 (Source file confio.c, line 725) Hexane-0.25nm3-index.gro: [ Hexane ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to define an index file
- Original Message - From: Moeed lecie...@googlemail.com Date: Wednesday, May 19, 2010 4:41 Subject: [gmx-users] how to define an index file To: gmx-users@gromacs.org Hello, I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system. To do this how should I define my index groups. Should I include all 125 molecuels in index file? now I have only the first 20 atoms (first molecule).. That depends what you want to measure. If you care about the magnitude of the interaction of any particular group of 20 with any other group, then you'll need each in a separate index group to create separate energy groups in your .mdp file. make_ndx -f Hexane-0.25nm3-index.gro -o index.ndx Reading structure file --- Program make_ndx, VERSION 4.0.7 Source code file: gmx_fatal.c, line: 511 Fatal error: Unexpected end of file in file Hexane-0.25nm3-index.gro at line 2 (Source file confio.c, line 725) Hexane-0.25nm3-index.gro: [ Hexane ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 You're doing something perverse. Give make_ndx -f your proper 125-hexane .gro file. See make_ndx -h for clues on what file formats are expected for what input parameters. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using g_densmap
Please use a descriptive subject line to help everybody.
I suspect your use editconf is your problem. -princ may not preserve your box
the way you've assumed. Try -princ -c, or editconf -princ then editconf -c.
It's also pointless and error-prone to compile MPI versions of the GROMACS
tools. Only mdrun is MPI-aware, and the installation guides make this clear.
Mark
- Original Message -
From: Ricardo Cuya Guizado rcu...@hotmail.com
Date: Wednesday, May 19, 2010 4:14
Subject: [gmx-users] RE: gmx-users Digest, Vol 73, Issue 109
To: gmx-users@gromacs.org
!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size:
10pt; font-family:Verdana } --
---
|
Dear Friends
I tried to obtain the XY density maps of the heme using g_densmap tool.
The molecule was centered in the box
The system was rotated to maintain the XY plane on the molecular plane.
In the reference gro file, the molecule was also centered and the plane XY
was on the molecular plane.
To create the reference gro file
editconf_mpi_d -f heme.gro -c -o heme_centered.gro -n index.ndx -princ
To center the molecule in the box
trjconv_mpi_d -f md10ns_heme.xtc -o md10ns_heme_centered.xtc -n index.ndx -s
dmpr.tpr -center -boxcenter rect -pbc atom
Rotations and translations were eliminated and the XY axis on the XY
molecular plane
trjconv_mpi_d -f md10ns_heme_centered.xtc -o
md10ns_heme_centrado_centered_rottrans.xtc -n index.ndx -s heme_centered.gro
-fit rot+trans
To obtain the XY density map
g_densmap_d -f md10ns_heme_centrado_centered_rottrans.xtc -s
heme_centered.gro -n index.ndx -o densmap.xpm
The result show the molecule in the corner of the figure and a diffuse withe
region around the molecule.
I will expect a more defined region around the molecule and centered.
I need help, thanks
Regards
Ricardo
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[gmx-users] energygrp_excl and grompp warning
Hi all, I try to use the energy exclusion keyword in the MDP file: energygrp_excl = CNT CNT and got the warning - WARNING 2 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups What can be the source of this issue? BTW, there are only LJ interactions between CNT and CNT according to the topology file. Thus this warning seems to be meaningless anyway. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energygrp_excl and grompp warning
Vitaly Chaban wrote: Hi all, I try to use the energy exclusion keyword in the MDP file: energygrp_excl = CNT CNT and got the warning - WARNING 2 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups What can be the source of this issue? Have a look here: http://lists.gromacs.org/pipermail/gmx-users/2006-May/021703.html -Justin BTW, there are only LJ interactions between CNT and CNT according to the topology file. Thus this warning seems to be meaningless anyway. Dr. Vitaly Chaban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how to define an index file
I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system. To do this how should I define my index groups. Should I include all 125 molecuels in index file? now I have only the first 20 atoms (first molecule).. To get the total interaction energy among your hexanes, all atoms of all C6H14's should be listed in the NDX file, e.g. 125 * 20... Good luck. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: how to define an index file
Vitaly Chaban wrote: I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system. To do this how should I define my index groups. Should I include all 125 molecuels in index file? now I have only the first 20 atoms (first molecule).. To get the total interaction energy among your hexanes, all atoms of all C6H14's should be listed in the NDX file, e.g. 125 * 20... The underlying issue with this approach is that there are then in excess of 125*125 energy terms written to the .edr file, which will quickly make this file very (perhaps prohibitively) large. Let the OP be warned... -Justin Good luck. Dr. Vitaly Chaban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] reading velocity in the g_msd routine
Hello gmx-users users :) I am modifying the 'g_msd' utility to be able to calculate viscosities using the corresponding Einstein relationship according to equation 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is similar to the mean-square displacement equation for self-diffusion coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy' where p_iy is the particle momenta in y-direction. So basically I need to be able to read both position and velocities from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and 'read_next_x' to read the coordinates. Can you please comment on how I can modify this code to read the corresponding velocities? Any help is greatly appreciated. thanks, Gaurav -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] reading velocity in the g_msd routine
On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel gauravgoel...@gmail.comwrote: Hello gmx-users users :) I am modifying the 'g_msd' utility to be able to calculate viscosities using the corresponding Einstein relationship according to equation 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is similar to the mean-square displacement equation for self-diffusion coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy' where p_iy is the particle momenta in y-direction. So basically I need to be able to read both position and velocities from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and 'read_next_x' to read the coordinates. Can you please comment on how I can modify this code to read the corresponding velocities? You could write your own little code to do that, see below for reading gro format http://manual.gromacs.org/current/online/gro.html amit Any help is greatly appreciated. thanks, Gaurav -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with index file
Hello, I am trying to create an index file to get interaction energies between hexane (C6H14, 20atoms) molecules (interaction energy between two hexane molecules) I have 125 hexane molecules in my system. Please help me figure out what the problem is. make_ndx -f Hexane-Stack125.gro -o index.ndx what I get from this command line is: Reading structure file Going to read 0 old index file(s) Analysing residue names: Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat There are: 125 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... 0 System : 2500 atoms 1 HEX : 2500 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit ** 1- Can you please help me understand what these mean? I just typed in q and exit. Then I typed in : grompp -f em18.mdp -c Hexane-Stack125.gro -n index.ndx -p Hexane-Stack125.top -o input.tpr and I got: Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Hexane' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Making dummy/rest group for T-Coupling containing 2500 elements Making dummy/rest group for Acceleration containing 2500 elements Making dummy/rest group for Freeze containing 2500 elements --- Program grompp, VERSION 4.0.7 Source code file: readir.c, line: 1007 Fatal error: Group Hexane not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. --- mdp file: title = Hexane cpp = /lib/cpp ;define = -DFLEX_SPC; This define statement is completely irrelevant if you're not dealing with water. constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 200 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 energygrps = Hexane Hexane index.ndx: [ System ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357
Re: [gmx-users] problem with index file
Moeed wrote:
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules (interaction energy between two hexane
molecules) I have 125 hexane molecules in my system. Please help me
figure out what the problem is.
make_ndx -f Hexane-Stack125.gro -o index.ndx
what I get from this command line is:
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
There are: 125 OTHER residues
There are: 0PROTEIN residues
There are: 0DNA residues
Analysing Other...
0 System : 2500 atoms
1 HEX : 2500 atoms
nr : group ! 'name' nr name 'splitch' nrEnter: list groups
'a': atom 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr'splitat' nr'h': help
'r': residue 'res' nr 'chain' char
name: group'case': case sensitive 'q': save and quit
**
1- Can you please help me understand what these mean? I just typed in
q and exit.
Doing this serves no purpose whatsoever. If you're keeping the default groups
that are already generated, there is no need for an index file. See the last
line on this page:
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
snip
---
Program grompp, VERSION 4.0.7
Source code file: readir.c, line: 1007
Fatal error:
Group Hexane not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.
---
mdp file:
title = Hexane
cpp = /lib/cpp
;define = -DFLEX_SPC; This define statement is
completely irrelevant if you're not dealing with water.
constraints = all-bonds
integrator = steep
dt = 0.002; ps !
nsteps = 200
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb= 1.0
rvdw= 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
energygrps = Hexane Hexane
Hexane is not a group, but HEX is. Furthermore, you're defining the same
group twice. The purpose of energygrps is to specify subsets of your system for
energy terms to be written. If your system is comprised of only hexane, there
is only one group to specify.
snip
2- I have a
question here: why the first group is named [system] and the second Hex?
See the link quoted above.
snip
I though maybe I should change the name in brackets. I renamed [system]
an d{HEX}to {Hexane] . I grompped again:
Don't. If you're naming multiple groups the same thing, then you've badly
broken the purpose of an index file. From what I can see, you do not need to be
using energygrps or index files at all!
snip
Fatal error:
Atom 1 in multiple Energy Mon. groups (1 and 2)
If the groups are redundant, then this makes sense.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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