Re: [gmx-users] Strangeness in gro file
On 13/09/2011 3:27 PM, Sweta Iyer wrote: Hi all, I am trying to use the g_membed tool to insert my protein into a DMPC membrane. My protein is a dimer and hence I separated the two monomers by a TER card in the original pdb file before pdb2gmx step for gromacs to identify it as teo separate entities.. I then merged my protein file with that of the membrane and added water and ions to it. Then when I went ahead to make an index file I notice that the numbering of residues is not continuous in my gro file, ie, it starts from residue 1-29 of a monomer, then again 1-29 of the second monomer, 1-128 for the DMPC moleculaes and similarly for the SOL and ions as well. As a result, I cannot exactly specify residue number for my index file to specify the two protein groups as different as the residue numbers overlap. Even when i try to do it, i get an error message saying Atom 1 in multiple T-Coupling groups Is there a way to re number them so that there is continuity or is there another way around to making the index file? I have not seen this the previously when I have made an index file. I am using gmx version 4.5.4 and the 53a6 forcefield. I am not attaching the gro file here as it is quite lengthy. Only atom numbering within a [moleculetype] is relative to that atom. Index files need atom numbers from the whole system. These are constructed from the first [molecules] entry being 1 to n, then the second [molecules] entry n+1 to n+n (if that entry is the same [moleculetype], etc. The numbers assigned to atoms and residues in the coordinate file supplied to grompp are ignored. Only the atom and molecule ordering is significant (and must match the .top). Do a grompp using an .mdp file that does not use any index groups (e.g. disable T-coupling), and pass that resulting .tpr to editconf to get a coordinate file back out. I expect the atom numbering will now be from 1 to N where N is the number of atoms in the system. Use that coordinate file to work out your index groups (with make_ndx or otherwise). Later, you and grompp will be talking the same language. :) 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist error
Mark, the command line goes like this- g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 the index file has group1- a_1322 ( this is just a single atom from a protein. its in sidechain) group2- a_OW ( this is water atoms) now as per the utility it should give me and output as- t:1 1322 a 54119 OW 0.389 but am getting something different On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 3:40 PM, aiswarya pawar wrote: Hi Mark, The -dist option says- print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1. That means it should give me the distance from OW to protein atom. If you choose correct groups that are correctly defined with respect to your trajectory and use a large enough distance cutoff. And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output- We can't tell. We don't know what your command line is, what's in your simulation system, the contents of your index groups, or which groups you've selected for which role. Clearly something is not working properly, and our time constraints mean that we're going to assume you've done something wrong, in the absence of evidence to the contrary. Mark t: 275 20230 SOL 62618 OW 0.341434 (nm) t: 275 22019 SOL 67985 OW 0.171584 (nm) t: 276 10768 SOL 34232 OW 0.303328 (nm) t: 276 20230 SOL 62618 OW 0.325176 (nm) t: 276 22019 SOL 67985 OW 0.187259 (nm) t: 277 10768 SOL 34232 OW 0.306008 (nm) t: 277 20230 SOL 62618 OW 0.326195 (nm) t: 277 22019 SOL 67985 OW 0.181089 (nm) t: 278 10768 SOL 34232 OW 0.274507 (nm) t: 278 22019 SOL 67985 OW 0.292652 (nm) t: 279 10618 SOL 33782 OW 0.319922 (nm) t: 280 10618 SOL 33782 OW 0.330082 (nm) t: 280 22019 SOL 67985 OW 0.330203 (nm) t: 281 8273 SOL 26747 OW 0.278731 (nm) t: 281 10618 SOL 33782 OW 0.325434 (nm) t: 281 11535 SOL 36533 OW 0.200327 (nm) t: 281 17036 SOL 53036 OW 0.343946 (nm) t: 282 8273 SOL 26747 OW 0.256558 (nm) t: 282 11535 SOL 36533 OW 0.327147 (nm) t: 283 8273 SOL 26747 OW 0.165061 (nm) t: 283 10618 SOL 33782 OW 0.306578 (nm) t: 283 17191 SOL 53501 OW 0.333075 (nm) t: 284 8273 SOL 26747 OW 0.19427 (nm) t: 284 10618 SOL 33782 OW 0.321927 (nm) t: 284 17191 SOL 53501 OW 0.30832 (nm) On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote: Iam -dist option because I need the distance between two groups That is not what g_dist -dist does. Please read g_dist -h. excluding -dist gives me X,Y,Z output which I don't want. And other output which you do, but you have to use -o to get it. Read g_dist -h. And am not specifying an -o. You need to specify -o to achieve your purpose. However, as I said quite a while ago, there is no value in measuring the distance between a protein phase and a water phase if they are in contact... Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Sender: gmx-users-boun...@gromacs.org Date: Mon, 12 Sep 2011 07:52:54 To: Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org gmx-users@gromacs.org Subject: Re: [gmx-users] g_dist error aiswarya pawar wrote: hi Justin, As far i referred the OW,HW1 etc are water atoms so how can it be distance between the SOL protein atoms, instead it is SOL water atoms. The printed distance indicates that there is a certain water molecule that is just over 2 hydrogen bonding lengths away from your protein's backbone. Sounds normal to me. -Justin Thanks On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu jalem...@vt.edu wrote: aiswarya pawar wrote:
[gmx-users] QM/MM/MD Semi-empirical Error
Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx407+mopac7, - Subscript out of range on file line 659, procedure moldat. Attempt to access the 0-th element of variable eheat. Aborted -- I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE
Hi Mark, I can confirm that the fix works. Setting -DGMX_ACCELERATION=Power6 sets to these /* Define to a macro mangling the given C identifier (in lower and upper case), which must not contain underscores, for linking with Fortran. */ #define F77_FUNC(name,NAME) name /* As F77_FUNC, but for C identifiers containing underscores. */ #define F77_FUNC_(name,NAME) name which do not gives the mentioned error. regards, PS: I'll report back if I find something else. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] how to handle different atom names between pdb and rtp files.
Hello, I've got a pdb file,but while I convert it to gro files, I met such problem: Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms I find that in the rtp files of the ff files, the H atom linked with C-alpha is called H, but in the pdb file, the same hydrogen atom is called HA, I think this may be the problem. So, my problem is, how to convert my pdb files to make the atom names consistent between the pdb and rtp files? KONG Xian Tsinghua University, Beijing, China 2011/9/13 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist error
On 13/09/2011 4:14 PM, aiswarya pawar wrote: Mark, the command line goes like this- g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 This command line is not using an index file. The index groups defined for the grompp that produced the .tpr are being used (which may be the default ones, depending what you did). Please copy and show the interactive input you made to g_dist after it showed the groups it knew about. the index file has group1- a_1322 ( this is just a single atom from a protein. its in sidechain) group2- a_OW ( this is water atoms) Your output is listing the time of the frame, and the residue number, residue name, atom number, and atom name of the matching atom. Apparently a water molecule can sometimes be closer than 0.2nm, and sometimes not. Mark now as per the utility it should give me and output as- t:1 1322 a 54119 OW 0.389 but am getting something different On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 13/09/2011 3:40 PM, aiswarya pawar wrote: Hi Mark, The -dist option says- print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1. That means it should give me the distance from OW to protein atom. If you choose correct groups that are correctly defined with respect to your trajectory and use a large enough distance cutoff. And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output- We can't tell. We don't know what your command line is, what's in your simulation system, the contents of your index groups, or which groups you've selected for which role. Clearly something is not working properly, and our time constraints mean that we're going to assume you've done something wrong, in the absence of evidence to the contrary. Mark t: 275 20230 SOL 62618 OW 0.341434 (nm) t: 275 22019 SOL 67985 OW 0.171584 (nm) t: 276 10768 SOL 34232 OW 0.303328 (nm) t: 276 20230 SOL 62618 OW 0.325176 (nm) t: 276 22019 SOL 67985 OW 0.187259 (nm) t: 277 10768 SOL 34232 OW 0.306008 (nm) t: 277 20230 SOL 62618 OW 0.326195 (nm) t: 277 22019 SOL 67985 OW 0.181089 (nm) t: 278 10768 SOL 34232 OW 0.274507 (nm) t: 278 22019 SOL 67985 OW 0.292652 (nm) t: 279 10618 SOL 33782 OW 0.319922 (nm) t: 280 10618 SOL 33782 OW 0.330082 (nm) t: 280 22019 SOL 67985 OW 0.330203 (nm) t: 281 8273 SOL 26747 OW 0.278731 (nm) t: 281 10618 SOL 33782 OW 0.325434 (nm) t: 281 11535 SOL 36533 OW 0.200327 (nm) t: 281 17036 SOL 53036 OW 0.343946 (nm) t: 282 8273 SOL 26747 OW 0.256558 (nm) t: 282 11535 SOL 36533 OW 0.327147 (nm) t: 283 8273 SOL 26747 OW 0.165061 (nm) t: 283 10618 SOL 33782 OW 0.306578 (nm) t: 283 17191 SOL 53501 OW 0.333075 (nm) t: 284 8273 SOL 26747 OW 0.19427 (nm) t: 284 10618 SOL 33782 OW 0.321927 (nm) t: 284 17191 SOL 53501 OW 0.30832 (nm) On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Iam -dist option because I need the distance between two groups That is not what g_dist -dist does. Please read g_dist -h. excluding -dist gives me X,Y,Z output which I don't want. And other output which you do, but you have to use -o to get it. Read g_dist -h. And am not specifying an -o. You need to specify -o to achieve your purpose. However, as I said quite a while ago, there is no value in measuring the distance between a protein phase and a water phase if they are in contact... Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To:aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org mailto:gmx-users@gromacs.org Reply-To:jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but
RE: [gmx-users] how to handle different atom names between pdb and rtp files.
dear Xian, open the PDB using text editor and replace the name... good luck From: xiansh...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Sep 2011 15:36:41 +0800 Subject: [gmx-users] how to handle different atom names between pdb and rtp files. Hello, I’ve got a pdb file,but while I convert it to gro files, I met such problem: Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms I find that in the rtp files of the ff files, the H atom linked with C-alpha is called H, but in the pdb file, the same hydrogen atom is called HA, I think this may be the problem. So, my problem is, how to convert my pdb files to make the atom names consistent between the pdb and rtp files? KONG Xian Tsinghua University, Beijing, China 2011/9/13 __ Information from ESET NOD32 Antivirus, version of virus signature database 6458 (20110912) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.com -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist error
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it takes the default index file, so there isnt any wrong in selecting the atoms. On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 4:14 PM, aiswarya pawar wrote: Mark, the command line goes like this- g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 This command line is not using an index file. The index groups defined for the grompp that produced the .tpr are being used (which may be the default ones, depending what you did). Please copy and show the interactive input you made to g_dist after it showed the groups it knew about. the index file has group1- a_1322 ( this is just a single atom from a protein. its in sidechain) group2- a_OW ( this is water atoms) Your output is listing the time of the frame, and the residue number, residue name, atom number, and atom name of the matching atom. Apparently a water molecule can sometimes be closer than 0.2nm, and sometimes not. Mark now as per the utility it should give me and output as- t:1 1322 a 54119 OW 0.389 but am getting something different On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 3:40 PM, aiswarya pawar wrote: Hi Mark, The -dist option says- print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1. That means it should give me the distance from OW to protein atom. If you choose correct groups that are correctly defined with respect to your trajectory and use a large enough distance cutoff. And when am already specifying only one atom from protein ie say 1322. why do i get this kind of output- We can't tell. We don't know what your command line is, what's in your simulation system, the contents of your index groups, or which groups you've selected for which role. Clearly something is not working properly, and our time constraints mean that we're going to assume you've done something wrong, in the absence of evidence to the contrary. Mark t: 275 20230 SOL 62618 OW 0.341434 (nm) t: 275 22019 SOL 67985 OW 0.171584 (nm) t: 276 10768 SOL 34232 OW 0.303328 (nm) t: 276 20230 SOL 62618 OW 0.325176 (nm) t: 276 22019 SOL 67985 OW 0.187259 (nm) t: 277 10768 SOL 34232 OW 0.306008 (nm) t: 277 20230 SOL 62618 OW 0.326195 (nm) t: 277 22019 SOL 67985 OW 0.181089 (nm) t: 278 10768 SOL 34232 OW 0.274507 (nm) t: 278 22019 SOL 67985 OW 0.292652 (nm) t: 279 10618 SOL 33782 OW 0.319922 (nm) t: 280 10618 SOL 33782 OW 0.330082 (nm) t: 280 22019 SOL 67985 OW 0.330203 (nm) t: 281 8273 SOL 26747 OW 0.278731 (nm) t: 281 10618 SOL 33782 OW 0.325434 (nm) t: 281 11535 SOL 36533 OW 0.200327 (nm) t: 281 17036 SOL 53036 OW 0.343946 (nm) t: 282 8273 SOL 26747 OW 0.256558 (nm) t: 282 11535 SOL 36533 OW 0.327147 (nm) t: 283 8273 SOL 26747 OW 0.165061 (nm) t: 283 10618 SOL 33782 OW 0.306578 (nm) t: 283 17191 SOL 53501 OW 0.333075 (nm) t: 284 8273 SOL 26747 OW 0.19427 (nm) t: 284 10618 SOL 33782 OW 0.321927 (nm) t: 284 17191 SOL 53501 OW 0.30832 (nm) On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote: Iam -dist option because I need the distance between two groups That is not what g_dist -dist does. Please read g_dist -h. excluding -dist gives me X,Y,Z output which I don't want. And other output which you do, but you have to use -o to get it. Read g_dist -h. And am not specifying an -o. You need to specify -o to achieve your purpose. However, as I said quite a while ago, there is no value in measuring the distance between a protein phase and a water phase if they are in contact... Mark Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Date: Mon, 12 Sep 2011 22:35:28 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org Reply-To: jalem...@vt.edu Subject: Re: [gmx-users] g_dist error aiswarya.pa...@gmail.com wrote: Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL. As was suggested several messages ago, please do NOT combine -o and -dist. If you want to measure a distance, use -o. If you want g_dist to print a list of atoms that satisfy some given criteria, use -dist, but not together. -Justin Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu Sender:
Re: [gmx-users] g_rms matrix between wt and mutant
Ok I tried that and it doesn't work: There's a fundamental difference between chains/no-chains topology, namely the existence of peptide bond between chains, and the different protonation state on the termini. In the chain-based topology there are several termini, and less peptide bonds. This causes the no-chains-tpr to have different number of atoms, and different protonation states. I tried using tpbconv to make a backbone-tpr, but it still gets me to segmentation fault. So thanks, but I don't think it would work. -SA On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching shay.teach...@gmail.comwrote: Thanks, I'll try that, and post again if it works. On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Shay Teaching wrote: When I try to work the command on a small portion of the backbone it seems to work just fine. But when I try the entire backbone (which is composed of several _separate_ chains) I am getting segmentation fault. Any workaround for that, so I can use the entire backbone? Are there chain identifiers separating the proteins? I don't know if that would cause the problem, but it's possible. In that case, I'd suggest you start with a coordinate file and topology without chain identifiers and generate a new .tpr file (and then take the backbone atoms only with tpbconv). -Justin Thanks again, -Shay On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Shay Teaching wrote: Hi all, (Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory and one mutant trajectory using the following command: g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n wt_backbone.ndx The file wt_backbone.ndx contains the backbone of the protein (Backbone indices are identical between wt and mutant). The result is that I am getting a well deserved error saying that wt.xtc and mutant.xtc has different number of atoms (the tpr itself): Fatal error: Second trajectory (76128 atoms) does not match the first one (76129 atoms) So the question becomes: Is there a (convenient) way to produce rms-matrix between wt and mutant? Or perhaps circumvent this problem in some other way? Use trjconv to write out new trajectories containing only backbone atoms of each protein, then use tpbconv to write a .tpr file with only backbone atoms in it (using index groups, if necessary). Then run g_rms again with these new trajectories and .tpr file. Everything should match if the indices are chosen correctly. -Justin -- ==**__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
Re: [gmx-users] g_rms matrix between wt and mutant
On 13/09/2011 6:11 PM, Shay Teaching wrote: Ok I tried that and it doesn't work: There's a fundamental difference between chains/no-chains topology, namely the existence of peptide bond between chains, and the different protonation state on the termini. In the chain-based topology there are several termini, and less peptide bonds. This causes the no-chains-tpr to have different number of atoms, and different protonation states. I tried using tpbconv to make a backbone-tpr, but it still gets me to segmentation fault. The idea behind Justin's original solution is still right. You need to provide two sets of corresponding atoms and those sets have to have the same size. So you need to construct two index groups that suit what you actually want to compare - say, the backbone atoms that are common to the two forms. That will require some thought, and playing around with make_ndx (or a text editor). Then use those to create subset .tpr and trajectory files as Justin suggested. Each form is likely to need its own customized index group to make the subset that is correct for it. Mark So thanks, but I don't think it would work. -SA On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching shay.teach...@gmail.com mailto:shay.teach...@gmail.com wrote: Thanks, I'll try that, and post again if it works. On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Shay Teaching wrote: When I try to work the command on a small portion of the backbone it seems to work just fine. But when I try the entire backbone (which is composed of several _separate_ chains) I am getting segmentation fault. Any workaround for that, so I can use the entire backbone? Are there chain identifiers separating the proteins? I don't know if that would cause the problem, but it's possible. In that case, I'd suggest you start with a coordinate file and topology without chain identifiers and generate a new .tpr file (and then take the backbone atoms only with tpbconv). -Justin Thanks again, -Shay On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Shay Teaching wrote: Hi all, (Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory and one mutant trajectory using the following command: g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n wt_backbone.ndx The file wt_backbone.ndx contains the backbone of the protein (Backbone indices are identical between wt and mutant). The result is that I am getting a well deserved error saying that wt.xtc and mutant.xtc has different number of atoms (the tpr itself): Fatal error: Second trajectory (76128 atoms) does not match the first one (76129 atoms) So the question becomes: Is there a (convenient) way to produce rms-matrix between wt and mutant? Or perhaps circumvent this problem in some other way? Use trjconv to write out new trajectories containing only backbone atoms of each protein, then use tpbconv to write a .tpr file with only backbone atoms in it (using index groups, if necessary). Then run g_rms again with these new trajectories and .tpr file. Everything should match if the indices are chosen correctly. -Justin -- ==__== 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.eduhttp://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-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
[gmx-users] gmx output in VMD
Dear Gmx users I have run MD on carbon nanotube with solvated drug molecules inside and outside the tubes. Kindly would you please let me know how I can visualize and calculate the amount of molecules only inside the carbon nanotube during MD process. May I know what keywords I should use in graph presentation? or Do you suggest any other software to solve this problem? Thank you very much Kind regards Meisam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] RE:g_lie
Message: 2 Date: Mon, 12 Sep 2011 18:38:57 +0300 From: ? ?? glapid...@gmail.com Subject: [gmx-users] g_lie (again..) To: gmx-users@gromacs.org Message-ID: CAB7OWN9sbMP+4XSaYF-ZNLZTy1Ve2e8cJ4pEb-RPdxc9P=y...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi all, Could anyone please refer to me to a paper or other resource that explains in detail (specifically technical) on how to preform g_lie. I know the matter has been brought up here quit often lately but looking through the mailing list archives and reference papaers (Aquist et al. and similar) tend to focus on the theory rather than practice. Thanks in advance, Gideon Just type it into the web, or pubmed.gov. I get 10 hits such as below. In addition, I back tracked the origional paper from slides or tutorials that reference the origional gromacs g_lie paper, but are somewhwere on the gromacs web page. Stephan Watkins J Mol Graph Model. 2006 Oct;25(2):176-85. Epub 2006 Jan 10. Predicting proteinase specificities from free energy calculations. Mekonnen SM, Olufsen M, Smalås AO, Brandsdal BO. -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] can i get the amber94 topology file for so4 molecule?
can i get the amber94 topology file for so4 molecule? -- Asha Jayachandran -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] gmx output in VMD
meisam valizadeh kiamahalleh wrote: Dear Gmx users I have run MD on carbon nanotube with solvated drug molecules inside and outside the tubes. Kindly would you please let me know how I can visualize and calculate the amount of molecules only inside the carbon nanotube during MD process. May I know what keywords I should use in graph presentation? or Do you suggest any other software to solve this problem? This is a question best posted to the VMD mailing list. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
Hi Yun, Have you read http://ambermd.org/formats.html? In particular, this note: NOTE: *the atom numbers in the following arrays that describe bonds, angles, and dihedrals are coordinate array indexes for runtime speed. The true atom number equals the absolute value of the number divided by three, plus one. In the case of the dihedrals, if the fourth atom is negative, this implies that the dihedral is an improper. If the third atom is negative, this implies that the end group interations are to be ignored. End group interactions are ignored, for example, in dihedrals of various ring systems (to prevent double counting of 1-4 interactions) and in multiterm dihedrals. * I may be failing to understand what you mean by GLYCAM force field assigns negative force constants to some dihedrals. Anyway, since GMX 4.5 can go without RB convertions, you can do this: acpype -x disac.inpcrd -p disac.prmtop --gmx45 If you have sander, you can do just one step of EM and compare against one step EM with GMX. Do the proper conversions and Energies diff should be 0.001%. Cheers, Alan On 12 September 2011 21:21, Yun Shi yunsh...@gmail.com wrote: Hi all, I am not a CS person, but I did find something in acpype.py as . if phase in [0, 180]: properDihedralsGmx45.append([item[0].atoms, phaseRaw, kPhi, period]) if not self.gmx45: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: .. kPhi here seems to be the dihedral force constant, and it seems if kPhi 0, no value will be assigned to C[0], C[1], C[2] ... I wonder if the negative dihedral force constants problem could be solved by changing 'kPhi 0' to 'kPhi != 0' for acpype? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Unsubscribe me Please
Unsubscribe me Please -- Om Prakash Sharma Ph.D Scholar DIT JRF Centre for Bioinformatics Pondicherry University Pondicherry-605014 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Unsubscribe me Please
om prakash wrote: Unsubscribe me Please Per the footer of every message that hits the list: Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_dist error
://www.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110913/23293b3e/attachment.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)
Dear Justin, Thanks a lot for your reply. Here I am providing the data and explaining the problem in detail: I hope that it will help you in understanding in a better way. Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm, so the tetramer (initial configuration) is approximately 16 nm and I have used a cubic box of 30 nm. Two groups (reference group and pull group) are decided on the basis of residue numbers forming 'ab' as reference grp and 'bc' as pull group by making an index file. I have verified that the initial configuration does not split across periodic boundaries, it is always inside the box throughout the simulation. Moreover, the initial distance is not equal to box vector. By g_dist , I have tried to calculate the distance between the two groups and it came out to be approx. 15 nm (Please have a look at the dist.xvg file at the end). Do you think that in the first ps time frame, should it get separated by 15 nm?? Please correct me if I have done anything wrong. By mistake, in my last mail I wrote that I need to pull along Y axis. In actual, it is Z-axis and I have used pull_dim N N Y. So it is just the mistake in writing the mail. Please let me know do you need any other data or parameters that I have used during this simulation. An early reply would me much appreciated. --- --- dist.xvg # This file was created Tue Sep 13 11:09:23 2011 # by the following command: # g_dist -f tub_pull.xtc -s tub_pull.tpr -n index.ndx # # g_dist is part of G R O M A C S: # # Giving Russians Opium May Alter Current Situation # @ title Distance @ xaxis label Time (ps) @ yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.000 15.0342455 -0.7714367 -0.9718266 14.9829559 0.500 15.0345469 -0.7726345 -0.9766102 -14.9828863 1.000 15.0345631 -0.7665710 -0.9862967 -14.9825792 1.500 15.0343399 -0.7575226 -0.9916229 14.9824638 2.000 15.0335970 -0.7490749 -0.9957008 -14.9818726 2.500 15.0322971 -0.7446661 -0.9996347 -14.9805260 3.000 15.0341187 -0.7364883 -1.0029345 -14.9825373 3.500 15.0331717 -0.7328205 -1.0078001 14.9814405 4.000 15.0311899 -0.7334194 -1.0118599 14.9791489 4.500 15.0334759 -0.7351160 -1.0128736 14.9812908 5.000 15.0336533 -0.7327585 -1.0102243 14.9817638 5.500 15.0327044 -0.7342167 -1.0076447 14.9809132 6.000 15.0335188 -0.7365904 -1.0090990 -14.9815168 6.500 15.0296631 -0.7375288 -1.0111809 -14.9774609 7.000 15.0294476 -0.7318525 -1.0155020 -14.9772310 7.500 15.0322533 -0.7323456 -1.0173597 -14.9798965 8.000 15.0353861 -0.7333517 -1.0172930 14.9829950 8.500 15.0323915 -0.7285290 -1.0122719 14.9805660 9.000 15.0284719 -0.7241497 -1.0072327 14.9771843 9.500 15.0285101 -0.7232113 -1.0051012 14.9774113 10.000 15.0306396 -0.7257242 -1.0020084 14.9796333 10.500 15.0324621 -0.7242069 -0.9959688 14.9819384 11.000 15.0324860 -0.7183657 -0.9881392 -14.9827623 11.500 15.0308609 -0.7121477 -0.9848318 -14.9816465 12.000 15.0318832 -0.7091122 -0.9842033 14.9828577 12.500 15.0316772 -0.7063818 -0.9834919 -14.9828262 13.000 15.0291939 -0.7024584 -0.9846754 -14.9804420 13.500 15.0307999 -0.7052488 -0.9864941 14.9818020 14.000 15.0286407 -0.7049980 -0.9902172 14.9794016 14.500 15.0301456 -0.7010813 -0.9916439 -14.9810019 15.000 15.0305882 -0.6967783 -0.9922857 -14.9816036 15.500 15.0319242 -0.6941795 -0.9950562 14.9828815 16.000 15.0315027 -0.6892128 -0.9928131 14.9828358 16.500 15.0314274 -0.6889334 -0.9883585 -14.9830685 17.000 15.0296593 -0.6906672 -0.9852924 14.9814167 17.500 15.0277662 -0.6964712 -0.9844646 -14.9793034 18.000 15.0301647
Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)
Shilpi Chaurasia wrote: Dear Justin, Thanks a lot for your reply. Here I am providing the data and explaining the problem in detail: I hope that it will help you in understanding in a better way. Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm, so the tetramer (initial configuration) is approximately 16 nm and I have used a cubic box of 30 nm. Two groups (reference group and pull group) are decided on the basis of residue numbers forming 'ab' as reference grp and 'bc' as pull group by making an index file. I will assume you mean CD here. If your groups are AB and BC, then you'll certainly have problems. I have verified that the initial configuration does not split across periodic boundaries, it is always inside the box throughout the simulation. Moreover, the initial distance is not equal to box vector. By g_dist , I have tried to calculate the distance between the two groups and it came out to be approx. 15 nm (Please have a look at the dist.xvg file at the end). Do you think that in the first ps time frame, should it get separated by 15 nm?? Please correct me if I have done anything wrong. If the dimer truly is together, then I would think this distance is too large unless (1) it actually is actually split across PBC, (2) your size calculations are wrong, or (3) your index groups are wrong. In any case, I can see this being a problem. A distance of 15 nm is 50% of the box size, and as soon as separation occurs, your pulling reference distance will be greater than 50% of the box vector, which causes a periodic distance to be calculated. Either use the distance_periodic pulling geometry or use a larger box. See below for a few thoughts on the dist.xvg data. By mistake, in my last mail I wrote that I need to pull along Y axis. In actual, it is Z-axis and I have used pull_dim N N Y. So it is just the mistake in writing the mail. Please let me know do you need any other data or parameters that I have used during this simulation. It would also be useful to know what grompp printed as the reference distance at time t=0. Here's why I think periodicity is indeed an issue: 0.000 15.0342455 -0.7714367 -0.9718266 14.9829559 0.500 15.0345469 -0.7726345 -0.9766102 -14.9828863 Note that within 0.5 ps, the sign of the z-distance has changed but the magnitude is basically the same. This indicates to me that your dimer is dancing back and forth across a periodic boundary. The output of pullx.xvg would also be informative to confirm this phenomenon. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE
Ok, Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during the compilation. Firstly, including config.h inside the fortran .F kernel files for power6 is causing problems with their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a modified xlf.cfg config file for XLF (cppoptions = -P, instead of -C) and pass it on with -F option and then add -qarch=pwr6 (all passed manually) for compilation of each power6 kernel .F file. That fixed the problem with the compilation of Power6 kernels part. Is there any more handy way of doing that? I've noticed that upon using Power6, cmake generates Fortran_DEFINES and Fortran_FLAGS inside src/gmxlib/CMakeFiles/gmx.dir/flags.make file. They somehow can not be modified from the command line. Same goes for the preprocessor flags. (-DCMAKE_CPP_FLAGS do not work?). Secondly, now I get something else: Linking C shared library libmd.so xlc: 1501-218 (W) file ../gmxlib/libgmx.so.6 contains an incorrect file suffix ../gmxlib/libgmx.so.6: In function `__bss_start': (*ABS*+0x1025cb00): multiple definition of `_edata' ../gmxlib/libgmx.so.6: In function `__data_start': (.data+0x8): multiple definition of `__dso_handle' /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtbeginS.o:(.data.rel+0x0): first defined here ../gmxlib/libgmx.so.6: In function `_fini': (.opd+0x30): multiple definition of `_fini' /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x18): first defined here ../gmxlib/libgmx.so.6: In function `_init': (.opd+0x18): multiple definition of `_init' /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x0): first defined here ../gmxlib/libgmx.so.6: In function `_end': (*ABS*+0x10268b20): multiple definition of `_end' ../gmxlib/libgmx.so.6: In function `__bss_start': (*ABS*+0x1025cb00): multiple definition of `__bss_start' /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtendS.o:(.dtors+0x0): multiple definition of `__DTOR_END__' ../gmxlib/libgmx.so.6:(.dtors+0x8): first defined here /usr/bin/ld: error in ../gmxlib/libgmx.so.6(.eh_frame); no .eh_frame_hdr table will be created. make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2 cheers, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE
On 14/09/2011 12:20 AM, Marcin Zielinski wrote: Ok, Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during the compilation. Firstly, including config.h inside the fortran .F kernel files for power6 is causing problems with their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a modified xlf.cfg config file for XLF (cppoptions = -P, instead of -C) and pass it on with -F option and then add -qarch=pwr6 (all passed manually) for compilation of each power6 kernel .F file. That fixed the problem with the compilation of Power6 kernels part. Is there any more handy way of doing that? I've noticed that upon using Power6, cmake generates Fortran_DEFINES and Fortran_FLAGS inside src/gmxlib/CMakeFiles/gmx.dir/flags.make file. They somehow can not be modified from the command line. Same goes for the preprocessor flags. (-DCMAKE_CPP_FLAGS do not work?). Secondly, now I get something else: Linking C shared library libmd.so xlc: 1501-218 (W) file ../gmxlib/libgmx.so.6 contains an incorrect file suffix ../gmxlib/libgmx.so.6: In function `__bss_start': (*ABS*+0x1025cb00): multiple definition of `_edata' ../gmxlib/libgmx.so.6: In function `__data_start': (.data+0x8): multiple definition of `__dso_handle' /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtbeginS.o:(.data.rel+0x0): first defined here ../gmxlib/libgmx.so.6: In function `_fini': (.opd+0x30): multiple definition of `_fini' /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x18): first defined here ../gmxlib/libgmx.so.6: In function `_init': (.opd+0x18): multiple definition of `_init' /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x0): first defined here ../gmxlib/libgmx.so.6: In function `_end': (*ABS*+0x10268b20): multiple definition of `_end' ../gmxlib/libgmx.so.6: In function `__bss_start': (*ABS*+0x1025cb00): multiple definition of `__bss_start' /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtendS.o:(.dtors+0x0): multiple definition of `__DTOR_END__' ../gmxlib/libgmx.so.6:(.dtors+0x8): first defined here /usr/bin/ld: error in ../gmxlib/libgmx.so.6(.eh_frame); no .eh_frame_hdr table will be created. make[2]: *** [src/mdlib/libmd.so.6] Error 1 make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2 make: *** [all] Error 2 Beats me, sorry. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Nucleic Acid in vacuo
Thank you very much for your help, Justin. I tried it with those mdp options: title = INITIAL_EM0 cpp = /lib/cpp constraints = all-bonds integrator = md rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 pbc = no This resulted in AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.88961e+016.04179e+015.60480e-043.74069e+01 -2.06394e+02 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 6.94305e-03 -5.66241e+01 -1.46290e+022.88457e-01 -1.46002e+02 Temperature Pressure (bar) Constr. rmsd 1.21730e+000.0e+000.0e+00 So, now the 1-4-values are slightly better (37.11 - 37.04 LJ, -207.7 - -206.3 Coulomb), while the SR-LJ and Coulomb energys are at two orders of magnitude too small (LJ: 0.7127 - 0.0069430, Coulomb: -4354.5 - -56.62). In fact, I considered looking through the code but wanted to avoid it because I fear that there are so much optimisations implemented in Gromacs that I probably will not understand whats going on and why. Maybe I will try it, but first I will play with the forcefield parameters to see what happens if I switch everything off except certain pairs, then I can compare them. Besides, I'm wondering, is there a way to disable all optimisations and just do a plain Lennard-Jones and Coulomb evaluation in vacuo without any box, solvent, boundary conditions and without cutoffs in Gromacs? Thanks and best regards, Matthias Am Montag, den 12.09.2011, 14:37 +0200 schrieb Justin A. Lemkul: Matthias Ernst wrote: Dear Gromacs users, I am currently working on porting forcefields from Gromacs to another program with the aim of simulating DNA. Therefore, I wrote a little script which reads in a PDB file, evaluates the Lennard-Jones and the Coulomb energy in vacuo with the forcefield data from Gromacs. I tried to implement the search for the neighbours by comparing inter-atomic distances to the van-der-Waals-radii and a flexible list-based factor weighting of the various contributions (where -1 is a default value, 0 is the atom itsself, 1 a bond to a next neighbour and so on, so my factor 3 should be equivalent to the 1-4-interaction in Gromacs). To verify what I have done, I tried to do a calculation of a single DA nucleic acid with Gromacs to compare the LJ and Coulomb energy. Unfortunately, the results do not match and I do not understand why. Please find the PDB code I used here http://pastebin.com/zB3sQHdZ and the python code I used for evaluating the potentials here http://pastebin.com/2v4nVdg3 The results I got with my code are - Total Lennard-Jones Energy [kJ/mol]: 0.712752493372 - Total 1-4-Lennard-Jones Energy [kJ/mol]: 37.1121824156 - Total Coulomb Energy [kJ/mol]: -4354.55160305 - Total Coulomb 1-4 Energy [kJ/mol]: -207.712332451 Using Gromacs, I got Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.00975e+016.05485e+014.28869e-043.69509e+01 -2.06010e+02 LJ (SR) Coulomb (SR) Potential Pressure (bar) Constr. rmsd -1.45022e+00 -5.67518e+01 -1.46615e+020.0e+001.80690e-04 The option in my mdp are title = INITIAL_EM0 cpp = /lib/cpp constraints = all-bonds integrator = steep nsteps = 50 nstcomm = 1 ns_type = grid rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 ; ; Energy minimizing stuff ; emtol = 1500.0 emstep = 0.01 Tcoupl = no Pcoupl = no gen_vel = no pbc = no I have not yet done a lot of calculations with Gromacs so maybe I did something wrong. If so, please correct me. You're better off with a single-point energy calculation, rather than a 50-step EM. Use the MD integrator with nsteps = 0 to compare configurations. If I recall, steepest descents makes a move before step zero, so you're not comparing the same quantities. What I wonder is that the 1-4-energies seem quite reasonable (LJ: 37.11 vs. 36.95, Coulomb -207.7 vs. -206.0) but the rest is rather different, especially the sign of the LJ term and the order of magnitude of the Coulomb term. Why is that? What does the SR in LJ and Coulomb in the Gromacs output mean? SR means short-range, i.e. within the cutoff. Since you've set all cutoffs to zero, this effectively means all interactions are calculated in this case. I can't offer an explanation for the different values observed, but I'll suggest you look into the Gromacs code to see how it calculates the energies and compare your program to see if you are, in fact, doing things the same way. -Justin --
Re: [gmx-users] Nucleic Acid in vacuo
Matthias Ernst wrote: Thank you very much for your help, Justin. I tried it with those mdp options: title = INITIAL_EM0 cpp = /lib/cpp constraints = all-bonds integrator = md rlist = 0.0 rcoulomb= 0.0 rvdw= 0.0 pbc = no This resulted in AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.88961e+016.04179e+015.60480e-043.74069e+01 -2.06394e+02 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy 6.94305e-03 -5.66241e+01 -1.46290e+022.88457e-01 -1.46002e+02 Temperature Pressure (bar) Constr. rmsd 1.21730e+000.0e+000.0e+00 So, now the 1-4-values are slightly better (37.11 - 37.04 LJ, -207.7 - -206.3 Coulomb), while the SR-LJ and Coulomb energys are at two orders of magnitude too small (LJ: 0.7127 - 0.0069430, Coulomb: -4354.5 - -56.62). In fact, I considered looking through the code but wanted to avoid it because I fear that there are so much optimisations implemented in Gromacs that I probably will not understand whats going on and why. Maybe I will try it, but first I will play with the forcefield parameters to see what happens if I switch everything off except certain pairs, then I can compare them. Besides, I'm wondering, is there a way to disable all optimisations and just do a plain Lennard-Jones and Coulomb evaluation in vacuo without any box, solvent, boundary conditions and without cutoffs in Gromacs? That's essentially what you're doing with the .mdp file above. No box (pbc = no), no cutoffs (r* = 0) and no solvent. There are options to disable optimizations and use generic kernels in Gromacs, but I can't recall all of them at the moment. Various environment variables are listed in the manual for disabling optimizations and in the configuration help description. -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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] QM/MM/MD Semi-empirical Error
Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx407+mopac7, Subscript out of range on file line 1002, procedure domldt. Attempt to access the 161-th element of variable labels. Aborted - Has anyone met this before? Thanks, yao - Forwarded Message - From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Tuesday, September 13, 2011 12:14 AM Subject: [gmx-users] QM/MM/MD Semi-empirical Error Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx407+mopac7, - Subscript out of range on file line 659, procedure moldat. Attempt to access the 0-th element of variable eheat. Aborted -- I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] phase transition in MD simulation
Dear experts, I am working on a pure polymer melt system under NPT and at a given T, pressure is increased up to around 1000 bar. However, the phase diagram of the polymer is indicating that at this T, as pressure is increased to above 500 bar, system falls below the melting point. I mean I am doing NPT on a liquid polymer by packing the chains in to the box but even applying a pressure of 1000 bar does not make the atoms or chains resemble a solid phase. The system would only become a more packed liquid phase. In other words, MD is representing an extrapolated liquid phase in the subcooled region. My question is whether there is any way to identify phase transition from MD simulation. Please comment and let me know what you think. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] phase transition in MD simulation
It certainly is, you just need to focus on a property that changes between the phases and that is obtainable from the MDSs. For a transition from liquid to solid, things like RDF, SDF, dihedral fractions and diffusion coefficients might provide some insight. You have the trajectories, why don't you just try as many of the properties you can get out of it and see if you see a change? Visual inspect is also a powerful technique, but you will need to back that up with some actual values. The averaging function in VMD can be quite handy for this, showing the average structure of a molecule over a particular time frame. Something you need to consider, is the time frame involved for a polymer to change between a liquid and solid state and the simulation time you have used. With having no idea on what polymer you have, size etc, I would hazard to say you would need easily something in the order of 200+ns to start to see some ordering occurring, if not something an order of magnitude longer. Polymers are big molecules and it will take long time for things to rearrange. And finally, the forcefield wont necessarily show the correct behaviour, unless it was derived to do that. It could simply be a poor model to use for showing phase behaviour. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Elisabeth Sent: Wednesday, 14 September 2011 11:33 AM To: Discussion list for GROMACS users Subject: [gmx-users] phase transition in MD simulation Dear experts, I am working on a pure polymer melt system under NPT and at a given T, pressure is increased up to around 1000 bar. However, the phase diagram of the polymer is indicating that at this T, as pressure is increased to above 500 bar, system falls below the melting point. I mean I am doing NPT on a liquid polymer by packing the chains in to the box but even applying a pressure of 1000 bar does not make the atoms or chains resemble a solid phase. The system would only become a more packed liquid phase. In other words, MD is representing an extrapolated liquid phase in the subcooled region. My question is whether there is any way to identify phase transition from MD simulation. Please comment and let me know what you think. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Time-varying Ion Charges
Hey Zach, You may be best off starting from the free energy code. It can be used to perturb charges and other things during a simulation. Hope it helps, Tsjerk On Sep 13, 2011 2:55 AM, Zach Levine zach.levine@gmail.com wrote: Hi everyone, I'm trying to implement time-varying charges for various ions located in ions.itp in GROMACS 4.5.4, but I'm not sure where to begin. I've already had some luck implementing AC external electric fields by modifying /src/mdlib/sim_util.c, but this required minimal work from me and a few strategically placed cosines. I have a feeling though that time-varying individual atomic charges will be considerably more difficult since I imagine GROMACS only reads from topol.top (and thus from ions.itp) just once at the beginning without updating the value, so I would likely have to import the time variable and recalculate the charge at every successive step. Since time is explicitly mentioned in the calc_f_el routine of sim_util.c (when I was dealing with external fields) I had no problems making this work there, but is it possible (or practical) to do the same thing with my static atomic charges as well? I've found some references to reading topol.top in /src/kernel/topio.c, and in theory I'd like to import, update, and export certain charges as a function of time, perhaps also in sim_util.c? I just don't know which files or variables to start importing in, or where the best place to implement this would be. Any ideas on this would be greatly appreciated, even if it's just keywords or significant variables for me to grep. Thanks, Zach -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] installation of FFTW
Hi I am working with RHEL 6 beta, I unable to install the FFTW package while installation I found the following error, make[3]: Leaving directory `/home/Ithayaraja/Desktop/ fftw-3.3.1-beta1/tools' make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools' Making all in m4 make[2]: Entering directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1' can you help me to find out where i did wrong? Thanks in advance -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] installation of FFTW
On 14/09/2011 3:24 PM, ITHAYARAJA wrote: Hi I am working with RHEL 6 beta, I unable to install the FFTW package while installation I found the following error, There is no error reported in what you have shown. make[3]: Leaving directory `/home/Ithayaraja/Desktop/ fftw-3.3.1-beta1/tools' make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools' Making all in m4 make[2]: Entering directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4' make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1' can you help me to find out where i did wrong? Not without knowing your configure line, knowing that you have followed the instructions on the GROMACS webpage, seeing what the actual error message was, and knowing why you're trying to use a beta of a version of FFTW that is a few years out of date. :) 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/Support/Mailing_Lists/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/Support/Mailing_Lists
