Re: [gmx-users] NVT conserved-energy lysozyme
On 15/05/2012 6:17 PM, David de Sancho wrote: Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling thermostat. Check out their paper and see what they claim for conservation properties. In step 6 of the tutorial an NVT equilibration is run using tcoupl = V-rescale. The temperature equilibrates quite rapidly as shown in Justin's webpage. Essentially, T fluctuates around its equilibrium value after ~ 2 ps. However looking at the conserved energy I find that there is a drift that does not seem to plateau even by the end of the 100 ps run (see attachment). Different observables equilibrate over different time scales. I have tried to sort this out myself by using the following settings: (1) change lincs_iter from 1 to 2. (2) change from PME to PME-Switch, which for NVE Gromacs recommends as more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4). (3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated. None of this seems to help. Actually Justin himself has helped me and found that with the following settings the conservation is considerably better === shift settings === vdwtype = shift coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.0 rvdw_switch = 0.8 Still there is a drift in the conserved quantity which seems a quite severe problem. Severe sounds like an over-description. The drift is 0.15% in the conserved quantity, beginning from a non-equilibrated starting point and only continuing for about the shortest equilibration period anybody could imagine using these days. There's a lot of approximations going on (PME, rigid bonds, static point charges) and maybe drift at this level is not significant. Still, it should get smaller if you just run for longer. 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] Two [ dihedrals ] sections in topology
On Tue, 2012-05-15 at 15:43 +0100, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Not that I'm aware of, and gromacs is designed to allow 2 dihedral blocks, I'd suggest you simply remove the block you do not want. Although you should be very sure that is what you want to do! Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? Not that I'm aware of; however, you should know that those missing parameters will be filled in with the dihedrals from the [ dihedral_types ] section above them in the .top file (this will most likely be in a #included file). [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field? I don't know them but they will be in the CHARMM27.ff/amioacids.rtp file which should be in $GMXDATA/gromacs/top/ Richard Thanks Greetings Lara - Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 12:57 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 15/05/2012 8:47 PM, Lara Bunte wrote: Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 119 8 5 6 8 910 5 Second block: [ dihedrals ] ; aiajakal functc0c1c2 c3 1 8 6 4 5180 100 1 2 4 5 5180 100 What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this? Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. In my .rtp file in the force field folder I have only this section for dihedrals [ impropers ] O4 N1 C2 N3 180 100 N1 C2 N3 H3 180 100 This produces your second block of type 5 dihedrals, given what you have said below. I declared my [ bondedtypes ] as the following: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. 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 -- 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] Two [ dihedrals ] sections in topology
On 5/15/12 10:43 AM, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Normally pdb2gmx will generate proper dihedrals based on bonded connectivity. Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? What you've been defining as empty is not necessarily so. The fact that parameters are not explicitly printed is not inherently indicative of a problem, since the parameters are looked up from ffbonded.itp and not necessarily recapitulated in the topology. If you get fatal errors about missing parameters, that's a separate issue. [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field? Look in charmm27.ff/aminoacids.rtp. -Justin -- Justin A. Lemkul, Ph.D. 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] topology file in DPPC
On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to find within my topology file (obtained by using pdb2gmx on my protein) #includegromos53a6.ff/forcefield.itpstatement so as to replace this line with #include gromos53a6_lipid.ff/forcefield.itp, as reported in the tutorial. Indeed, at the top of my topology file I have got; ; Include forcefield parameters #include ffG53a6.itp and, after the list of all atoms, at the bottom of the file; ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name PHOSPHOLIPASE A2, AMMODYTOXIN A [ molecules ] ; Compound#mols Protein_A 1 I'm wondering if it may depend on the fact I have got the version gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change some options when I launch the command pdb2gmx in order to build my topology file. I used the following command: pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro -p 3G8G_membr.top -i 3G8G_membr.itp -ignh -water spc and I chose GROMOS96 53A6 Please, let me know. The problem is you're using an old version. The tutorial states that you are expected to be using a version in the 4.5.x series. If you don't, then the procedure will be somewhat different. -Justin -- Justin A. Lemkul, Ph.D. 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] parameters and restrains for Fe3+
Hi, I need to introduce new atomtypes/parameters and restrains in Gromacs for Fe3+. Could you please inform me on how can I do it? Thanks. Cheers, Carla -- View this message in context: http://gromacs.5086.n6.nabble.com/parameters-and-restrains-for-Fe3-tp4981309.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] my e-mail to post in this list
my e-mail to post in this list is : carla.carluc...@libero.it -- 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] about trifloroehanol
Thank you Justin .. I will follow your Instructions .. With Best Wishes, R.David -- 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] topology file in DPPC
Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to find within my topology file (obtained by using pdb2gmx on my protein) #includegromos53a6.ff/forcefield.itpstatement so as to replace this line with #include gromos53a6_lipid.ff/forcefield.itp, as reported in the tutorial. Indeed, at the top of my topology file I have got; ; Include forcefield parameters #include ffG53a6.itp and, after the list of all atoms, at the bottom of the file; ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name PHOSPHOLIPASE A2, AMMODYTOXIN A [ molecules ] ; Compound#mols Protein_A 1 I'm wondering if it may depend on the fact I have got the version gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change some options when I launch the command pdb2gmx in order to build my topology file. I used the following command: pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro -p 3G8G_membr.top -i 3G8G_membr.itp -ignh -water spc and I chose GROMOS96 53A6 Please, let me know. Silvia -- 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] topology file in DPPC
Do you know where I should look to find the solution to my problem? Silvia On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to find within my topology file (obtained by using pdb2gmx on my protein) #includegromos53a6.ff/forcefield.itpstatement so as to replace this line with #include gromos53a6_lipid.ff/forcefield.itp, as reported in the tutorial. Indeed, at the top of my topology file I have got; ; Include forcefield parameters #include ffG53a6.itp and, after the list of all atoms, at the bottom of the file; ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name PHOSPHOLIPASE A2, AMMODYTOXIN A [ molecules ] ; Compound#mols Protein_A 1 I'm wondering if it may depend on the fact I have got the version gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change some options when I launch the command pdb2gmx in order to build my topology file. I used the following command: pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro -p 3G8G_membr.top -i 3G8G_membr.itp -ignh -water spc and I chose GROMOS96 53A6 Please, let me know. The problem is you're using an old version. The tutorial states that you are expected to be using a version in the 4.5.x series. If you don't, then the procedure will be somewhat different. -Justin -- Justin A. Lemkul, Ph.D. 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 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] topology file in DPPC
On 5/15/12 11:11 AM, scapr...@uniroma3.it wrote: Do you know where I should look to find the solution to my problem? The entire procedure for modifying the force field is different, as the directory structure and file names are very different. The best solution is to upgrade your Gromacs version and follow the tutorial directly. -Justin -- Justin A. Lemkul, Ph.D. 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] about trifloroehanol
Thank you justin.. I will try to adhere spacing -- 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] Two [ dihedrals ] sections in topology
Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field? Thanks Greetings Lara - Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 12:57 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 15/05/2012 8:47 PM, Lara Bunte wrote: Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 19 8 5 6 8 9 10 5 Second block: [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 1 8 6 4 5 180 100 1 2 4 5 5 180 100 What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this? Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. In my .rtp file in the force field folder I have only this section for dihedrals [ impropers ] O4 N1 C2 N3 180 100 N1 C2 N3 H3 180 100 This produces your second block of type 5 dihedrals, given what you have said below. I declared my [ bondedtypes ] as the following: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. Mark -- 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] about trifloroehanol
On 5/15/12 8:25 AM, rama david wrote: Hi all Very sorry for my stupid question .. I really work a lot on these problem I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT H 0.41000 0 OT OTFE-0.62500 0 CH2T CHTFE 0.27300 0 CT CTFE 0.45200 0 F1T FTFE-0.17000 0 F2T FTFE-0.17000 0 F3T FTFE-0.17000 0 [ bonds ] HTOTgb_1 OT CH2Tgb_18 CH2TCTgb_27 CT F1Tgb_13 CT F2Tgb_13 CT F3Tgb_13 [ angles ] ; aiajak gromos type HTOT CH2T ga_50 OT CH2TCT ga_51 CH2TCT F1T ga_52 CH2TCT F2T ga_52 CH2TCT F3T ga_52 F1TCT F2T ga_49 F1TCT F3T ga_49 F2TCT F3T ga_49 [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type HTOT CH2TCT gd_24 I draw TFE with Avogadro software... I get following pdb .. COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 C LIG 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F LIG 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F LIG 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F LIG 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 O LIG 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7 H LIG 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8 H LIG 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 H LIG 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END I change pdb as follow to match the nomenclature with G96 53a6 ff (Is it right or wrong ) OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 CT TFE 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 CH2T TFE 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F1T TFE 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F2T TFE 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F3T TFE 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 OT TFE 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7H TFE 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8H TFE 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 HT TFE 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 AFTER running pdb2gmx -ignh I got following error -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue 'F' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried a lot ... Please give me some suggestion ... Thank you in Advance ... The column spacing of a .pdb file is fixed and you must adhere to it. The changes you have made look fine, but they are spaced incorrectly, thus pdb2gmx is not able to correctly read its contents. -Justin -- Justin A. Lemkul, Ph.D. 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] NVT conserved-energy lysozyme
Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling thermostat. In step 6 of the tutorial an NVT equilibration is run using tcoupl = V-rescale. The temperature equilibrates quite rapidly as shown in Justin's webpage. Essentially, T fluctuates around its equilibrium value after ~ 2 ps. However looking at the conserved energy I find that there is a drift that does not seem to plateau even by the end of the 100 ps run (see attachment). I have tried to sort this out myself by using the following settings: (1) change lincs_iter from 1 to 2. (2) change from PME to PME-Switch, which for NVE Gromacs recommends as more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4). (3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated. None of this seems to help. Actually Justin himself has helped me and found that with the following settings the conservation is considerably better === shift settings === vdwtype = shift coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.0 rvdw_switch = 0.8 Still there is a drift in the conserved quantity which seems a quite severe problem. Can anyone give some pointers on how to sort this out? Thanks -David attachment: equil_nvt.png-- 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] ATB SWISSPARAM Topologies
Thanks a lot Justin! On Tue, May 15, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/15/12 5:54 AM, Anirban wrote: Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome. I would always verify parameters before running real production simulations. I believe ATB and SwissParam are, in general, far more reliable than PRODRG, but I doubt it can be stated universally that any automated method is inherently flawless. -Justin -- ==**== Justin A. Lemkul, Ph.D. 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 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_Listshttp://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] Problem in visualizing protein-ion complex trajectory in vmd
Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using vmd, I am encountering some problems. 1) While using the -pbc flag with whole option, the protein is visualized properly, but the Mg and GTP are showing jumps moving away from the protein structure. That is why, the distance between Mg, GTP with atoms of the protein is not coming out properly. 2) While using the -pbc flag with nojump option, the protein is visible in stretched and distorted geometry, but the Mg and GTP are intact with the structure. Here, the distance between Mg,GTP with atoms of the protein is calculated correctly. 3) Then, I tried with both the whole and nojump options,used in succession (first whole and then nojump), but still the protein is not visualized properly. It is visible in stretched geometry only, as was visible with nojump. Can anyone help me regarding the problems I am facing with the visualization? Any help will be highly appreciated. Thanks in advance Regards, Neeru -- 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] NVT conserved-energy lysozyme
On Tue, 2012-05-15 at 09:17 +0100, David de Sancho wrote: Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. Compiled in double or single precision ? If the latter one is the case, perhaps numerical errors are the reason for the large energy drift. /Flo My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling thermostat. In step 6 of the tutorial an NVT equilibration is run using tcoupl = V-rescale. The temperature equilibrates quite rapidly as shown in Justin's webpage. Essentially, T fluctuates around its equilibrium value after ~ 2 ps. However looking at the conserved energy I find that there is a drift that does not seem to plateau even by the end of the 100 ps run (see attachment). I have tried to sort this out myself by using the following settings: (1) change lincs_iter from 1 to 2. (2) change from PME to PME-Switch, which for NVE Gromacs recommends as more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4). (3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated. None of this seems to help. Actually Justin himself has helped me and found that with the following settings the conservation is considerably better === shift settings === vdwtype = shift coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.0 rvdw_switch = 0.8 Still there is a drift in the conserved quantity which seems a quite severe problem. Can anyone give some pointers on how to sort this out? Thanks -David -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] Generating_tpr_file from.xtc
Hi Shahid, You probably have a matching .top file lying around? You can use it with the .gro file to regenerate the .tpr. Note that most analysis can also be run with a .gro/.pdb file. Cheers, Tsjerk On Tue, May 15, 2012 at 4:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/15/12 10:28 AM, shahid nayeem wrote: Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. No. None of those files have the required topology information. -Justin -- Justin A. Lemkul, Ph.D. 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 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Generating_tpr_file from.xtc
On 5/15/12 10:28 AM, shahid nayeem wrote: Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. No. None of those files have the required topology information. -Justin -- Justin A. Lemkul, Ph.D. 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] Test Particle Insertion
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
It is not not divided by nm3. The legend for y axis is not appropriate
for your plot. Keep in mind that the same graph is used to represent
lots of quantities (you can plot all of them with xmgrace -nxy tpi.xvg).
The y axis is not the same for all, but only one label is possible, so
developers have to chose which label to place on the axis. But this is
just a label, don't give much importance to it and analyse you results
(including units) according to the equations and the standard units in
gromacs.
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
The volume appears in the expression of the excess chemical potential if
you are running a NpT ensemble. The second plot (if you use xmgrace -nxy
tpi.xvg) does not contain the volume.
3. The value corresponds to the plateau so I should run it for longer
time?
You are getting a timeensemble average and for large sampling (and
large simulation times), this average should converge. So, the final
value you will get is the last point of the graph, it up to you to say
if it is converged. So you can try to enlarge the number of points
sampled, if the shape does not change you are sampling correctly every
snapshot, then take longer simulation times if you want to converge your
results.
Javier
El 15/05/12 09:57, Steven Neumann escribió:
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical
potential? The tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@xaxis label Time (ps)
@yaxis label (kJ mol\S-1\N) / (nm\S3\N)
Can anyone explain me these legends? I just want obtain a
value of the excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this
and what are the
units? kJ/mol? Please, explain as the above letters does not
mean to me anything?
These strings are formatted for XmGrace. Have you tried plotting
the file to see what it contains? The legends will be far more
obvious if you do.
-Justin
Thank you Justin.
Can anyone explain me from the plot:
http://speedy.sh/Xpnws/tpi.JPG
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
3. The value corresponds to the plateau so I should run it for longer
time?
Thank you,
Steven
--
Justin A. Lemkul, Ph.D.
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/justin
--
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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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Re: [gmx-users] about the frame selection
On Tue, May 15, 2012 at 11:26 AM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs Users , I simulated a 4 peptide in a box . After completion of 30 ns simulattion , I extract the particular time frame 29000 ps of my interest. Now I want these frame for my next simulations study .. In one simulation I want to keep the box size same as the mentioned in extracted pdb and in another one I need to change the size of box to 70 70 70 REMARKGENERATED BY TRJCONV TITLE Protein in water t= 29000.0 REMARKTHIS IS A SIMULATION BOX CRYST1 45.096 45.096 45.096 90.00 90.00 90.00 P 1 1 MODEL1 So my queries are like 1. Should I used the extracted frame directly for further study or I need to remove the periodicity...?? I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. 2 . to change the box size how to proceed ?? Should I delete the line manually and adjust the box size You can change the box dimensions with editconf using the -box (desired dimensions) option. -Anirban All suggestion are welcome ... Than you in advance rama david -- 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] about trifloroehanol
Hi all Very sorry for my stupid question .. I really work a lot on these problem I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT H 0.41000 0 OT OTFE-0.62500 0 CH2T CHTFE 0.27300 0 CT CTFE 0.45200 0 F1T FTFE-0.17000 0 F2T FTFE-0.17000 0 F3T FTFE-0.17000 0 [ bonds ] HTOTgb_1 OT CH2Tgb_18 CH2TCTgb_27 CT F1Tgb_13 CT F2Tgb_13 CT F3Tgb_13 [ angles ] ; aiajak gromos type HTOT CH2T ga_50 OT CH2TCT ga_51 CH2TCT F1T ga_52 CH2TCT F2T ga_52 CH2TCT F3T ga_52 F1TCT F2T ga_49 F1TCT F3T ga_49 F2TCT F3T ga_49 [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type HTOT CH2TCT gd_24 I draw TFE with Avogadro software... I get following pdb .. COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 C LIG 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F LIG 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F LIG 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F LIG 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 O LIG 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7 H LIG 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8 H LIG 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 H LIG 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END I change pdb as follow to match the nomenclature with G96 53a6 ff (Is it right or wrong ) OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 CT TFE 1 -7.301 3.857 0.070 1.00 0.00 C HETATM2 CH2T TFE 1 -6.798 2.416 0.102 1.00 0.00 C HETATM3 F1T TFE 1 -8.626 3.915 0.327 1.00 0.00 F HETATM4 F2T TFE 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM5 F3T TFE 1 -6.668 4.631 0.977 1.00 0.00 F HETATM6 OT TFE 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM7H TFE 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM8H TFE 1 -6.898 2.006 1.111 1.00 0.00 H HETATM9 HT TFE 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT12345 AFTER running pdb2gmx -ignh I got following error -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue 'F' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried a lot ... Please give me some suggestion ... Thank you in Advance ... Rama David ... -- 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] about trifloroehanol
On 5/15/12 9:54 AM, rama david wrote: Hi to all Sorry Justin , I try to correct spacing but now it stuck to another problem pdb to TFE is as follow OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C ATOM 2 CH2T TFE 1 -6.061 1.111 0.155 1.00 0.00 C ATOM 3 F1T TFE 1 -5.017 2.899 1.300 1.00 0.00 F ATOM 4 F2T TFE 1 -6.461 3.426 -0.251 1.00 0.00 F ATOM 5 F3T TFE 1 -4.506 2.627 -0.806 1.00 0.00 F ATOM 6 OT TFE 1 -7.065 0.921 1.164 1.00 0.00 O ATOM 7H TFE 1 -5.248 0.409 0.367 1.00 0.00 H ATOM 8H TFE 1 -6.500 0.837 -0.808 1.00 0.00 H ATOM 9 HT TFE 1 -6.742 1.339 1.982 1.00 0.00 H The spacing in this file is still potentially problematic. CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END after giving pdb2gmx -ignh If you delete the two extraneous H atoms in the .pdb file and omit -ignh, you won't have this problem. It give following error WARNING: atom HT is missing in residue TFE 1 in the pdb file You might need to add atom HT to the hydrogen database of building block TFE in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- now I know go with missing is wrong ..But to check error I goes with -missing flag . the output confo.gro is as follow UNNAMED 6 1TFE OT1 -0.706 0.092 0.116 1TFE CH2T2 -0.606 0.111 0.015 1TFE CT3 -0.551 0.253 0.009 1TFEF1T4 -0.502 0.290 0.130 1TFEF2T5 -0.646 0.343 -0.025 1TFEF3T6 -0.451 0.263 -0.081 0.25590 0.25050 0.21060 The hydrogen attched to oxyge is missing .. The entry to these hydrogen as HT is mentioned in pdb file ... The warning message is self-explanatory. I will be a very greatfull to you if you told me how to add HT in aminoacids.hdb Aminoacids.hdb file is as follow SER 2 11HN-CCA 12HGOGCBCA *TFE 1 12HOCH2C* The corrected line would read: 12HTOTCH2TCT This is a small bug that should probably be fixed, though in your case, with proper input, use of the .hdb file is unnecessary. -Justin -- Justin A. Lemkul, Ph.D. 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] DNA persistence length with g_polystat
Dear Gromacs users, I am doing MD simulation of DNA oligomers and need to calculate their persistence length. Using g_polystat with -p persist.xvg I discovered that the output file contains a lot of nan values among other values of numbers of bonds. As far as I understood reading this forum, there were other people who also had nan-problems using g_polystat. Is there a bug in g_polystat function or I am doing something wrong? I am using DNA index group that I believe is appropriate for calculation of DNA backbone persistence length. Thank you! -- View this message in context: http://gromacs.5086.n6.nabble.com/DNA-persistence-length-with-g-polystat-tp4981293.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] about trifloroehanol
Hi to all Sorry Justin , I try to correct spacing but now it stuck to another problem pdb to TFE is as follow OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C ATOM 2 CH2T TFE 1 -6.061 1.111 0.155 1.00 0.00 C ATOM 3 F1T TFE 1 -5.017 2.899 1.300 1.00 0.00 F ATOM 4 F2T TFE 1 -6.461 3.426 -0.251 1.00 0.00 F ATOM 5 F3T TFE 1 -4.506 2.627 -0.806 1.00 0.00 F ATOM 6 OT TFE 1 -7.065 0.921 1.164 1.00 0.00 O ATOM 7H TFE 1 -5.248 0.409 0.367 1.00 0.00 H ATOM 8H TFE 1 -6.500 0.837 -0.808 1.00 0.00 H ATOM 9 HT TFE 1 -6.742 1.339 1.982 1.00 0.00 H CONECT12345 CONECT1 CONECT21678 CONECT2 CONECT31 CONECT41 CONECT51 CONECT629 CONECT72 CONECT82 CONECT96 MASTER000000009090 END after giving pdb2gmx -ignh It give following error WARNING: atom HT is missing in residue TFE 1 in the pdb file You might need to add atom HT to the hydrogen database of building block TFE in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463 Fatal error: There were 1 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- --- now I know go with missing is wrong ..But to check error I goes with -missing flag . the output confo.gro is as follow UNNAMED 6 1TFE OT1 -0.706 0.092 0.116 1TFE CH2T2 -0.606 0.111 0.015 1TFE CT3 -0.551 0.253 0.009 1TFEF1T4 -0.502 0.290 0.130 1TFEF2T5 -0.646 0.343 -0.025 1TFEF3T6 -0.451 0.263 -0.081 0.25590 0.25050 0.21060 The hydrogen attched to oxyge is missing .. The entry to these hydrogen as HT is mentioned in pdb file ... The warning message is self-explanatory. I will be a very greatfull to you if you told me how to add HT in aminoacids.hdb Aminoacids.hdb file is as follow SER 2 11HN-CCA 12HGOGCBCA *TFE 1 12HOCH2C* THR 2 11HN-CCA 12HG1OG1CBCA TRP 7 11HN-CCA 11HD1CD1CGNE1 So What line I have to add here??? Please suggest me the way out to get rid from error .. Rama David -- 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] about the frame selection
On Tue, May 15, 2012 at 11:59 AM, Anirban reach.anirban.gh...@gmail.comwrote: Thank you Anirban I proceed as you mentioned... -- 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 calculate the center of the mass in gromacs
Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. Thanks a lot. -- 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] Generating_tpr_file from.xtc
Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. 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/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] about the frame selection
Thank you ANIRBAN for your reply .. I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. Could you told me how to remove the periodicity ??? Thank you 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/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] Test Particle Insertion
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@xaxis label Time (ps)
@yaxis label (kJ mol\S-1\N) / (nm\S3\N)
Can anyone explain me these legends? I just want obtain a value of the
excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this and what are
the
units? kJ/mol? Please, explain as the above letters does not mean to me
anything?
These strings are formatted for XmGrace. Have you tried plotting the file
to see what it contains? The legends will be far more obvious if you do.
-Justin
Thank you Justin.
Can anyone explain me from the plot:
http://speedy.sh/Xpnws/tpi.JPG
1. Why this value is divided by nm3? Shall I multiply it by the simulation
box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess chemical
potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
3. The value corresponds to the plateau so I should run it for longer time?
Thank you,
Steven
--
==**==
Justin A. Lemkul, Ph.D.
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
==**==
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Re: [gmx-users] about the frame selection
On Tue, May 15, 2012 at 11:48 AM, rama david ramadavidgr...@gmail.comwrote: Thank you ANIRBAN for your reply .. I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. Could you told me how to remove the periodicity ??? You can use trjconv with -pbc mol -ur compact options. But first look into trjconv -h -Anirban Thank you 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/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] Re: NVT conserved-energy lysozyme
Thanks Florian and Mark for your replies. I have run the simulation for longer (one order of magnitude longer, i.e. 1 ns) and what I get now is that the 'conserved energy' follows its drift linearly. Now, of course, we are speaking about 1.2% drift/ns in the value of the energy, which seems quite substantial. http://gromacs.5086.n6.nabble.com/file/n4981453/equil_nvt.png Second, I have compiled and run with double precision. Although the value for the conserved energy is slightly different, the slope of E vs time is essentially identical. -- View this message in context: http://gromacs.5086.n6.nabble.com/NVT-conserved-energy-lysozyme-tp4980918p4981453.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] ATB SWISSPARAM Topologies
Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome. Thanks and 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/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] Problem in visualizing protein-ion complex trajectory in vmd
On 15/05/2012 10:22 PM, neeru sharma wrote: Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using vmd, I am encountering some problems. 1) While using the -pbc flag with whole option, the protein is visualized properly, but the Mg and GTP are showing jumps moving away from the protein structure. That is why, the distance between Mg, GTP with atoms of the protein is not coming out properly. 2) While using the -pbc flag with nojump option, the protein is visible in stretched and distorted geometry, but the Mg and GTP are intact with the structure. Here, the distance between Mg,GTP with atoms of the protein is calculated correctly. 3) Then, I tried with both the whole and nojump options,used in succession (first whole and then nojump), but still the protein is not visualized properly. It is visible in stretched geometry only, as was visible with nojump. Can anyone help me regarding the problems I am facing with the visualization? Any help will be highly appreciated. See suggestions here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. You will perhaps need to identify a frame where everything is in the box, and then choose a suitable (new?) group for the various operations, or do multiple passes with trjconv. 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
[gmx-users] about the frame selection
Hi Gromacs Users , I simulated a 4 peptide in a box . After completion of 30 ns simulattion , I extract the particular time frame 29000 ps of my interest. Now I want these frame for my next simulations study .. In one simulation I want to keep the box size same as the mentioned in extracted pdb and in another one I need to change the size of box to 70 70 70 REMARKGENERATED BY TRJCONV TITLE Protein in water t= 29000.0 REMARKTHIS IS A SIMULATION BOX CRYST1 45.096 45.096 45.096 90.00 90.00 90.00 P 1 1 MODEL1 So my queries are like 1. Should I used the extracted frame directly for further study or I need to remove the periodicity...?? 2 . to change the box size how to proceed ?? Should I delete the line manually and adjust the box size All suggestion are welcome ... Than you in advance rama david -- 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] Two [ dihedrals ] sections in topology
On 15/05/2012 8:47 PM, Lara Bunte wrote: Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 119 8 5 6 8 910 5 Second block: [ dihedrals ] ; aiajakal functc0c1c2 c3 1 8 6 4 5180 100 1 2 4 5 5180 100 What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this? Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. In my .rtp file in the force field folder I have only this section for dihedrals [ impropers ] O4 N1 C2 N3 180 100 N1 C2 N3 H3 180 100 This produces your second block of type 5 dihedrals, given what you have said below. I declared my [ bondedtypes ] as the following: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. 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
[gmx-users] itp file for flavins
Does anyone have itp files for oxidized, reduced and semiquinone states of FMN (flavin mononucleotide)? I noticed gromacs is supposed to have rtp files for flavins, not sure how to access that. Thanks Vijaya Date: Tue, 15 May 2012 08:50:35 -0700 From: daviddesan...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Re: NVT conserved-energy lysozyme Thanks Florian and Mark for your replies. I have run the simulation for longer (one order of magnitude longer, i.e. 1 ns) and what I get now is that the 'conserved energy' follows its drift linearly. Now, of course, we are speaking about 1.2% drift/ns in the value of the energy, which seems quite substantial. http://gromacs.5086.n6.nabble.com/file/n4981453/equil_nvt.png Second, I have compiled and run with double precision. Although the value for the conserved energy is slightly different, the slope of E vs time is essentially identical. -- View this message in context: http://gromacs.5086.n6.nabble.com/NVT-conserved-energy-lysozyme-tp4980918p4981453.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Two [ dihedrals ] sections in topology
Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 19 8 5 6 8 9 10 5 Second block: [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 1 8 6 4 5 180 100 1 2 4 5 5 180 100 What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this? In my .rtp file in the force field folder I have only this section for dihedrals [ impropers ] O4 N1 C2 N3 180 100 N1 C2 N3 H3 180 100 I declared my [ bondedtypes ] as the following: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Thanks for help Greetings -- 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] TFE Proper Dihedral types...
Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing following error grompp -f minim.mdp -c mix.pdb -o em.tpr -p final.top ERROR 1 [file topol-tef.itp, line 46]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 1372 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I checked the topology for TFE, Dihedral section is as follow ... * [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 4 1gd_24 2 3 4 5 1* So what to resolve the problem .. All suggestions are welcome... I will be a very greatfull to help Thank you 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/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] ATB SWISSPARAM Topologies
On 5/15/12 5:54 AM, Anirban wrote: Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome. I would always verify parameters before running real production simulations. I believe ATB and SwissParam are, in general, far more reliable than PRODRG, but I doubt it can be stated universally that any automated method is inherently flawless. -Justin -- Justin A. Lemkul, Ph.D. 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] How to calculate the center of the mass in gromacs
On 5/15/12 11:35 AM, xu zhijun wrote: Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. This is a function of g_traj. -Justin -- Justin A. Lemkul, Ph.D. 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] itp file for flavins
Please do not reply to an existing thread to ask a new question; start a new thread instead. On 5/15/12 12:03 PM, vijaya subramanian wrote: Does anyone have itp files for oxidized, reduced and semiquinone states of FMN (flavin mononucleotide)? I noticed gromacs is supposed to have rtp files for flavins, not sure how to access that. The .rtp files are pdb2gmx input files, such that if you have a coordinate file containing one of these residues, it will produce a topology. It is the same mechanism used for macromolecules like proteins and DNA. -Justin -- Justin A. Lemkul, Ph.D. 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] TFE Proper Dihedral types...
On 5/15/12 12:14 PM, rama david wrote: Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing following error grompp -f minim.mdp -c mix.pdb -o em.tpr -p final.top ERROR 1 [file topol-tef.itp, line 46]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 1372 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I checked the topology for TFE, Dihedral section is as follow ... * [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 1 2 3 4 1gd_24 2 3 4 5 1 * So what to resolve the problem .. All suggestions are welcome... The parameters are missing from ffbonded.itp, making the implementation incomplete. You can obtain a TFE topology from ATB: http://compbio.biosci.uq.edu.au/atb/download.py?molid=1655 -Justin -- Justin A. Lemkul, Ph.D. 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] How to calculate the center of the mass in gromacs
Thanks a lot, Justin. It works well. Jerry --- On Tue, 5/15/12, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] How to calculate the center of the mass in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, May 15, 2012, 12:51 PM On 5/15/12 11:35 AM, xu zhijun wrote: Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. This is a function of g_traj. -Justin -- Justin A. Lemkul, Ph.D. 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 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] Questions about Thermostats
Hello To make better energy minimization procedures I read about thermostats and barostats. I understand the physical concepts and differences between global and local thermostats and the difference between Berendsen and Nose-Hoover thermostat. 1.) Maybe this question is a little bit hairsplitting, but: This concepts of thermostats and barostats, is this Thermodynamics, is this Kinetics, is this statistical physics? What is it if I want to give this a name. 2.) I read, that local thermostats, i.e. stochastic dynamics produce a NVT ensemble, which is a canonical ensemble and that this alway fulfills Ergodicity Theorem. About this I have following question: In my literature they said, that this means, that all degrees of freedom in the system are coupled strong enough each other. This confuses me. I learned, that ergodicity means, that the complete phase space is passed by a trajectory, if we wait long enough. This means, that ensemble average is equal to time average of the system. Where is in my statement about ergodicity the meaning of all degrees of freedom in the system are coupled strong enough Do this in fact mean, that the complete phase space is passed? 3.) I ask myself what I should use. First question: Local or global thermostat? I guess (not knowing, guessing), that global is better for energy minimization, because as far as I understand, it is more stable than local description. From a physical point of view I think Nose-Hoover shoul be always better, because it produces a real canonical ensemble, while Berendsen is microcanonical ensemble, which is totaly unrealistic?! In an microcanonical ensemble, energy is not changed with the enviroment. This makes no sense? Thanks for helping me Greetings Lara -- 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] Two [ dihedrals ] sections in topology
Hi Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. Greetings - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 17:02 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/15/12 10:43 AM, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Normally pdb2gmx will generate proper dihedrals based on bonded connectivity. Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? What you've been defining as empty is not necessarily so. The fact that parameters are not explicitly printed is not inherently indicative of a problem, since the parameters are looked up from ffbonded.itp and not necessarily recapitulated in the topology. If you get fatal errors about missing parameters, that's a separate issue. [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field? Look in charmm27.ff/aminoacids.rtp. -Justin -- Justin A. Lemkul, Ph.D. 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] Measure angle with g_sgangle
Hey. I'm using Gromacs to simulate a transmembrane-peptide and would like to measure the angle between three residues of the protein. The protein gets during the simulation a kink of about 87°. I would like to measure the real angle of the kink with g_sgangle. So I made an index file and defined two groups with: a 5|a 248 name 17 group1 and a 248|a 477 name 18 group2 The atom numbers are the C alpha atom of the N terminus, the AS where the kink is located and the C terminus. Now I used g_sgangle to measure the angle between this two groups with: g_sgangle -f md_27nstrjconv.trr -n g_sgangle.ndx -s md_27ns.tpr -oa sg_angle.xvg Then I've chosen group1 and group2 (17 18). The sg_angle.xvg looks like that: @title Angle between group1 and group2 @xaxis label Time (ps) @yaxis label Angle (degrees) @TYPE xy 0 0.200158 78.4538 10 0.224148 77.0472 20 0.25729 75.0907 30 0.237989 76.2321 40 0.250923 75.4679 50 0.232999 76.5263 60 0.267666 74.4746 70 0.227826 76.8309 80 0.286902 73.3274 90 0.250226 75.5091 100 0.254623 75.2488 ... So it tells me that Gromacs measured an angle of about 0.2??! Can anyone tell me what I am doing wrong? And what tells me the third column of the .xvg file? Thilo-- 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] Measure angle with g_sgangle
On 5/15/12 2:47 PM, Mast, Thilo wrote: Hey. I'm using Gromacs to simulate a transmembrane-peptide and would like to measure the angle between three residues of the protein. The protein gets during the simulation a kink of about 87°. I would like to measure the real angle of the kink with g_sgangle. So I made an index file and defined two groups with: a 5|a 248 name 17 group1 and a 248|a 477 name 18 group2 The atom numbers are the C alpha atom of the N terminus, the AS where the kink is located and the C terminus. Now I used g_sgangle to measure the angle between this two groups with: g_sgangle -f md_27nstrjconv.trr -n g_sgangle.ndx -s md_27ns.tpr -oa sg_angle.xvg Then I've chosen group1 and group2 (17 18). The sg_angle.xvg looks like that: @title Angle between group1 and group2 @xaxis label Time (ps) @yaxis label Angle (degrees) @TYPE xy 0 0.200158 78.4538 10 0.224148 77.0472 20 0.25729 75.0907 30 0.237989 76.2321 40 0.250923 75.4679 50 0.232999 76.5263 60 0.267666 74.4746 70 0.227826 76.8309 80 0.286902 73.3274 90 0.250226 75.5091 100 0.254623 75.2488 ... So it tells me that Gromacs measured an angle of about 0.2??! Can anyone tell me what I am doing wrong? And what tells me the third column of the .xvg file? The second column is the cosine of the angle. The third column is the actual angle. -Justin -- Justin A. Lemkul, Ph.D. 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] Two [ dihedrals ] sections in topology
On 5/15/12 2:53 PM, Lara Bunte wrote: Hi Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. Please see my previous replies regarding what you're calling empty dihedrals. There's nothing necessarily wrong with them (unless they raise an error), and if pdb2gmx created them then they almost certainly need to be present. Each rotatable bond has a dihedral term associated with it, even if it's not something you thought of previously or defined explicitly in the .rtp entry. -Justin -- Justin A. Lemkul, Ph.D. 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] itp file for flavins
On 5/15/12 5:37 PM, vijaya subramanian wrote: Hi I found all the rtp files-aminoacid.rtp,dna.rtp but not fmnr.rtp which is in ffgmx.rtp according to the gromacs building blocks site. I need to look at the fmnr.rtp file to match atom names. Individual molecules generally do not have their own .rtp files. The parameters you need are in aminoacids.rtp: $ grep FMN g*.ff/*.rtp gmx.ff/aminoacids.rtp:[ FMNO ] gmx.ff/aminoacids.rtp:[ FMNR ] gmx.ff/aminoacids.rtp:[ FMNS ] gromos43a1.ff/aminoacids.rtp:[ FMNO ] gromos43a1.ff/aminoacids.rtp:[ FMNS ] gromos43a1.ff/aminoacids.rtp:[ FMNR ] gromos43a2.ff/aminoacids.rtp:[ FMNO ] gromos43a2.ff/aminoacids.rtp:[ FMNS ] gromos43a2.ff/aminoacids.rtp:[ FMNR ] gromos45a3.ff/aminoacids.rtp:[ FMNO ] gromos45a3.ff/aminoacids.rtp:[ FMNS ] gromos45a3.ff/aminoacids.rtp:[ FMNR ] gromos53a5.ff/aminoacids.rtp:[ FMNO ] gromos53a5.ff/aminoacids.rtp:[ FMNS ] gromos53a5.ff/aminoacids.rtp:[ FMNR ] gromos53a6.ff/aminoacids.rtp:[ FMNO ] gromos53a6.ff/aminoacids.rtp:[ FMNS ] gromos53a6.ff/aminoacids.rtp:[ FMNR ] I would recommend not using gmx.ff, for reasons described in the manual. The newer versions of Gromos96 are more suitable. -Justin -- Justin A. Lemkul, Ph.D. 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] Two [ dihedrals ] sections in topology
On 16/05/2012 4:53 AM, Lara Bunte wrote: Hi Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. An empty block of dihedrals doesn't hurt, but you don't have one of these. A block of dihedrals lacking parameters gets those parameters looked up from ffbonded.itp. You likely can't have only improper dihedrals and expect any resemblance to the behaviour of the CHARMM27 forcefield. It sounds to me like you're trying to do something that might not be worth attempting, but this thread hasn't revealed your objective. There's no point moving deckchairs on the Titanic if there's icebergs all around. Mark Greetings - Ursprüngliche Message - Von: Justin A. Lemkuljalem...@vt.edu An: Lara Buntelara.bu...@yahoo.de; Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 17:02 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/15/12 10:43 AM, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Normally pdb2gmx will generate proper dihedrals based on bonded connectivity. Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology? What you've been defining as empty is not necessarily so. The fact that parameters are not explicitly printed is not inherently indicative of a problem, since the parameters are looked up from ffbonded.itp and not necessarily recapitulated in the topology. If you get fatal errors about missing parameters, that's a separate issue. [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 5 5 Those are angle, dihedral and improper function types that are abnormal for CHARMM27. Using these in your .rtp means that you are no longer using CHARMM27. It might be reasonable for you to do this, but you need to be absolutely sure why. Importing a topology from another force field is not an acceptable reason. What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field? Look in charmm27.ff/aminoacids.rtp. -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] What is the subroutine for SHAKE or RATTLE? Thanks.
Hi, everyone. It is my first use of Gromacs and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Kevin Len Department of Materials Science Fudan University 220 Handan Road Shanghai, CHINA, 200433-- 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] TFE Proper Dihedral types...
On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: The parameters are missing from ffbonded.itp, making the implementation incomplete. You can obtain a TFE topology from ATB: http://compbio.biosci.uq.edu.**au/atb/download.py?molid=1655http://compbio.biosci.uq.edu.au/atb/download.py?molid=1655 -Justin Thank you Justin .. I obtain the topology from given link.. 1. If you have some time , Could you tell me the way how to fix the missing parameter from ffbonded.itp ..??? With Best Wishes, Rama David -- 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] Coupling groups in protein-ligand-lipid simulation
Hi ALL, I am simulating a membrane protein docked with a ligand and embedded in a lipid bilayer. For COM removal I am using two groups, Prt_Lig_Lipid and SOL_CL. For temperature and pressure couplings should I use these two groups or should I use three groups, Protein, Lipid and Lig_SOL_CL? Any suggestion is welcome. Thanks and 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/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 can i specify a user defined potential between i, i+2 residues
Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. T -- 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] Fwd: How can i specify a user defined potential between i, i+2 residues
Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Thanks for a reply in advance, with regards, Mohan -- 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] How can i specify a user defined potential between i, i+2 residues
On 16/05/2012 3:43 PM, mohan maruthi sena wrote: Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Doing that with a user-defined non-bonded potential requires you change nrexcl for your force field. Doing that with a user-defined bonded potential doesn't, but you'll have to specify all the interactions manually. 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] What is the subroutine for SHAKE or RATTLE? Thanks.
On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs http://lammps.sandia.gov/ and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs http://lammps.sandia.gov/. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. 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
