[gmx-users] Energetics of ion and subatrate binding sites
Dear Gromacs Users, I have simulated a protein with different ions and same substrate bound to it in POPC lipid bilayer using Groamcs 4.5.4. The ion binding and substrate binding sites are coupled. After Md simulation we see a reorganization of these sites. Now, we are trying to calculate the energetics of these ion and substrate binding sites. Could any one please suggest ideas or methods to do the same in Gromacs package? Please let me know. Thanks Pramod -- 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] Occupancy for a distance cut off
Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. Thanks, Pramod -- 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] Occupancy for a distance cut off
Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Thanks, Pramod On Mon, Feb 11, 2013 at 7:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/11/13 6:15 PM, ram bio wrote: Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.5 Å) between ion and a particular residue atom during simulation. Please suggest. g_dist -dist 0.35 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Occupancy for a distance cut off
Thank you!! On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/11/13 9:16 PM, ram bio wrote: Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o N101Cbest2NACL606S336HG1.xvg and the output was distance calculated for every 10 frames in nm as under: t: 11870 336 SER 4166 HG1 0.239086 (nm) t: 11880 336 SER 4166 HG1 0.248868 (nm) t: 11890 336 SER 4166 HG1 0.231819 (nm) t: 11900 336 SER 4166 HG1 0.218495 (nm) t: 11910 336 SER 4166 HG1 0.233166 (nm) t: 11920 336 SER 4166 HG1 0.283512 (nm) t: 11930 336 SER 4166 HG1 0.239512 (nm) t: 11940 336 SER 4166 HG1 0.216938 (nm) t: 11950 336 SER 4166 HG1 0.220066 (nm) t: 11960 336 SER 4166 HG1 0.227595 (nm) t: 11970 336 SER 4166 HG1 0.247895 (nm) t: 11980 336 SER 4166 HG1 0.259074 (nm) t: 11990 336 SER 4166 HG1 0.228319 (nm) t: 12000 336 SER 4166 HG1 0.264722 (nm) So, my question is that now do maths and find percent frames that were above the 3.5 Å and expresses it relation to unity for occupancy. That is if i have 30 frames above 3.5Å out of 100, then the occupancy would be 0.7. Please advice if there is any other ways to do it.. Redirect the output into a file, count the number of lines in the file with wc -l and you have the answer. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
[gmx-users] barium ion simulation
Dear Gromacs Users, I am trying to simulate a protein in lipid bilayer with a barium ion binding pocket in it, with Charmm27 FF in gromacs 4.5.4. I found that barium ion is not included under charmm27 ff ions.itp. I was wondering if there is any way to simulate protein with barium bound using gromacs and charmm27 ff? Thanks Pramod -- 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] xmgrace graphs
Thanks On Wed, Oct 3, 2012 at 6:04 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 12:06 AM, naga sundar wrote: Dear Pramod use the command xmgrace -nxy file1.xvg file2.xvg Instead of file1 and file2 use ur file name. Distance plots produced by g_dist have four data sets (distance and x,y,z components) so plotting in this way can be quite messy. Leave out the -nxy if you want to only plot the total distance and not the remaining (x,y,z) components. -Justin On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
[gmx-users] xmgrace graphs
Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- 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] Ca ion simulation incorporated in protein structure
Dear Gromacs Users, I am trying to simulate a modeled protein -ligand complex in lipid bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose which is to see the effect of substitution of ions (Ca instead of Na ions) in the protein structure on protein ligand interactions , I have modeled the protein with Ca ions in the protein instead of Na ions. For the same, I was wondering if Gromacs 4.5.4 with Charmm27 FF can simulate Ca ions if incorporated in the protein instead of Na ions as i described here. Thanks and Regards, Pramod -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] charmm 27 gromacs version mdp query
Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so I want to know your any suggestions and corrections in my mdp files (below), so that i can use the corrected mdp file to simulate the system. *1st mdp file :* title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions coulombtype= PME rlist = 1.2; neighborlist cut-off rcoulomb = 1.2; Coulomb cut-off rvdw = 1.2; VdW cut-off fourierspacing = 0.12; The maximum grid spacing for the FFT grid when using PPPM or PME pme_order = 4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 2nd mdp file: title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 Your help is highly appreciated. Thanks Pramod -- 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] charmm 27 FF mdp query
Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so I want to know your any suggestions and corrections in my mdp files (below), so that i can use the corrected mdp file to simulate the system. *1st mdp file :* title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions coulombtype= PME rlist = 1.2; neighborlist cut-off rcoulomb = 1.2; Coulomb cut-off rvdw = 1.2; VdW cut-off fourierspacing = 0.12; The maximum grid spacing for the FFT grid when using PPPM or PME pme_order = 4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 2nd mdp file: title = Bilayer-500 cpp= /lib/cpp constraints= all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 200 ; 4 ns nstcomm= 1 nstxout= 5000 nstvout= 5000 nstfout= 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist= 10 ; long range interactions rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps= protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.01.0 compressibility= 4.5e-5 4.5e-5 ref_p = 1.01.0 gen_vel= yes gen_temp = 303.0 gen_seed = 478905 Your help is highly appreciated. Thanks Pramod -- 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] unknown cmap torsion between atoms
Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381 8394 8397. Could someone please explain me what this error mean and how to overcome this. thanks, Pramod -- 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] unknown cmap torsion between atoms
Hi Mark, Thanks for the response. I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot show any error. Cant the charmm gui built system be used in gromacs with charmm27ff. Out of the 134 atoms for each popc in the structure file few initial atoms were not matching in the lipids.itp file under charmmff folder, so i changed the atom names in the lipid.itp under popc section to match with atom names in the structure file, is that could be reason? moreover, grompp also throws error as no default U-B types along with unknown CMAP torsion. Could you please diagnose where the problem exists in my procedure and let me know. Thanks Pramod On Mon, Oct 31, 2011 at 9:57 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/11/2011 1:24 PM, ram bio wrote: Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381 8394 8397. Could someone please explain me what this error mean and how to overcome this. It means you are somehow using CMAP on a dihedral whose atom types do not have a known CMAP function - unknown CMAP torsion. You need to do some detective work on those atoms and their types to work out why. Mark -- 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] POPC bilayer with Charmmff
Dear Gromacs users, I have downloaded the POPC bilayer molecular coordinates with charmmff equilibrated from Dr. Klauda's website. In this site it is mentioned Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 with vdw ForceSwitching turned on; what does vdw ForceSwitching turned on mean, is it related to adding few more parameters to mdp files? like rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 and , does this apply to gromacs also, if i use these lipid bilayers to run simulations in gromacs. I have one more question, i want to increase this bilayer containing 72 lipids to 250 lipids, so how can i do this or can i get it downloaded from any website like Dr.Klauda website Please let me know your suggestions. Thanks, Pramod -- 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] pdb2gmx charmm topology lipid
Dear Justin, Thanks for the suggestions. The lipids are built into the CHARMM27 implementation in Gromacs. You can generate their topology with pdb2gmx. Run pdb2gmx on a single lipid, convert it to an .itp file, and #include it in the topology. I separated out one lipid from the POPC bilayer (250 lipids) i am having (attached -popc.pdb) and modified (popcatomtype.pdb) the atom names as per the /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp file. Then i executed pdb2gmx -f popcatomtype.pdb -o popcatom.gro choosing option 8 for Charmm ff 1 for water model but, i am getting an error as below: Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b Reading popcatomtype.pdb... Read 52 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. There are 1 chains and 0 blocks of water and 0 residues with 52 atoms chain #res #atoms 1 'C' 1 52 WARNING: there were 0 atoms with zero occupancy and 52 atoms with occupancy unequal to one (out of 52 atoms). Check your pdb file. Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm27) Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp Residue 41 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp Residue 45 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp Residue 57 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp Residue 61 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.30# Processing chain 1 'C' (52 atoms, 1 residues) There are 1 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue POP0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'POP' 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 --- Please let me know your suggestions to fix this error. Thanks, Pramod On Wed, Oct 12, 2011 at 8:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. I think significantly more parameters than just dihedrals need to be altered to make the Berger united-atom force field compatible with OPLS. While searching for the literature on compatibility of lipid FF and protein FF, I found few references where similar modification was done for DOPC lipid bilayer and were suitable with various FF for proteins and also with CHARMM FF: 1. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields.J Comput Chem 32: 1400–1410, 2011. I don't have the lipid bilayer with their itp files with CHARMM FF parameterization. Please could you inform me where to obtain them, so that i can use the lipid bilayer structure for embedding the protein and use the related CHARMM FF parameterised itp in the topology file in gromacs for MD simulation. The lipids are built into the CHARMM27 implementation in Gromacs. You can generate their topology with pdb2gmx. Run
[gmx-users] mktop
Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation. Thanks, Pramod -- 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
Fwd: [gmx-users] mktop
Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors : grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr ERROR 1 [file ligand.itp, line 291]: No default Ryckaert-Bell. types .. --- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1526 Fatal error: [ file ligand.itp, line 397 ]: Atom index (0) in dihedrals out of bounds (1-53). This probably means that you have inserted topology section dihedrals in a part belonging to a different molecule than you intended to. In that case move the dihedrals section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The commands executed to reach the grompp step are as follows: pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb editconf -f processlig.pdb -o procent.pdb -princ editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr I have attached the topol.top, ligand.itp files for your information, Please let me know your suggestions to fix this error. Thanks, Pramod On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging the output of mktop into gromacs MD simulation. You can #include any molecule topology in a system .top, provided you have the right format: http://www.gromacs.org/**Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File There is no tutorial for using mktop with a protein-ligand/membrane system, but there are tutorials for protein-ligand complexes: http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/complex/index.**htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html and membrane protein systems: http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/membrane_**protein/index.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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 ligand.itp Description: Binary data topol.top Description: Binary data -- 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] mktop
Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and As per Gromacs website: Note that an .itp filehttp://www.gromacs.org/Documentation/File_Formats/.itp_Filewill be specific to a given force field, and will only function when included by a .top filehttp://www.gromacs.org/Documentation/File_Formats/.top_Filethat has previously included the .itp files http://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the #define and #ifdef mechanisms can permit the same .itp filehttp://www.gromacs.org/Documentation/File_Formats/.itp_Fileto work with multiple force fields, e.g. share/top/water.itp. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used with opls. It was informed by swiss param team that the ligand parameters generated by swissparam could also be used with opls FF in principle as they are based on MMFF So, in order to cross check or validate my results i was trying to use mktop to generate the ligand topologies for MD simulations. Please let me know your comments and suggestions on the procedure , regarding the compatibility of MMFF generated topologies to be used by OPLS and other methods to validate my results. Thanks, Pramod On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file generated from the pdb2gmx. During the pdb2gmx command, i used opls FF. The coordinates of ligand used as input for mktop were added to the output of pdb2gmx (process.pdb - only protein coordinates), so that the structure file along with ligand coordinates (processlig.pdb) can be used for further steps. I doubt whether the procedure followed by me is correct, as when i execute grompp command to add ions i am getting errors : grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr ERROR 1 [file ligand.itp, line 291]: No default Ryckaert-Bell. types .. --**- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1526 Fatal error: [ file ligand.itp, line 397 ]: Atom index (0) in dihedrals out of bounds (1-53). This probably means that you have inserted topology section dihedrals in a part belonging to a different molecule than you intended to. In that case move the dihedrals section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- The commands executed to reach the grompp step are as follows: pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb editconf -f processlig.pdb -o procent.pdb -princ editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p topol.top grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr I have attached the topol.top, ligand.itp and procentsolv.gro files for your information, Please let me know your suggestions to fix this error. The ligand.itp file is trash. Most of your atoms have zero charge (except for a few that have +/- 1...yikes!) and on line 397 (as cited in the error message) atom 0 is referenced, which of course does not exist, since numbering starts with 1. You also have some exotic atom types present, and thus bonded parameters cannot be assigned, as grompp complained earlier. You need a better quality topology, and perhaps a different force field that might be suited for doing these simulations. -Justin Thanks
Re: [gmx-users] mktop
Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. Please let me know your comments and suggestions regarding the procedure followed and the itp files usage for gromacs MD simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I understand that. The program did a poor job, per the reasons I cited before. I do not know anything about mktop (other than what it does), so I cannot analyze its suitability here, but due to missing parameters and bogus charges, you should not use that topology for anything. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not? I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). As per Gromacs website: Note that an .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File will be specific to a given force field, and will only function when included by a .top file http://www.gromacs.org/** Documentation/File_Formats/.**top_Filehttp://www.gromacs.org/Documentation/File_Formats/.top_File that has previously included the .itp files http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the |#define| and |#ifdef| mechanisms can permit the same .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File to work with multiple force fields, e.g. |share/top/water.itp|. Note the key caveat here - through the use of #define and #ifdef you can make use of different force fields. That means you can control which parameters are applied based on different conditions. I could write an .itp file for any molecule that has force field parameters for any force field, and all I'd have to do is enclose all relevant directives within #ifdef blocks and it would work. This note does *not* indicate that you can mix and match force fields. Doing so is generally a very bad idea, if it even works syntactically. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used with opls
Re: [gmx-users] mktop/swissparam
Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. Please let me know your comments and suggestions regarding the procedure followed and the itp files usage for gromacs MD simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during md simulations in lipid bi layer. I found that MKTOP can generate topology files using opls ff for small molecules. I understand that. The program did a poor job, per the reasons I cited before. I do not know anything about mktop (other than what it does), so I cannot analyze its suitability here, but due to missing parameters and bogus charges, you should not use that topology for anything. I have also tried swiss param to generate the ligand parameters to be used in protein ligand simulation using gromacs. The force field i am using for simulations is OPLS. My ligand contains an azido group and a tropane ring with protonated nitrogen. SwissParam force field has been designed to be compatible with the Charmm force field, but they are not tested on opls.Using the ligand topologies from swissparam, i was able to run the MD simulations using gromacs with opls without errors (swissparam - gromacs tutorial), only issues being the charges on the ligand, so i generated various input files (mol2 files) for swissparam with charges generated using ambcc1, gastergier and MMFF. But the itp files obtained from swissparam had same charges for the ligand atoms irrespective of the input provided i.e. charged or uncharged mol2 files, and If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not? I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). As per Gromacs website: Note that an .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File will be specific to a given force field, and will only function when included by a .top file http://www.gromacs.org/** Documentation/File_Formats/.**top_Filehttp://www.gromacs.org/Documentation/File_Formats/.top_File that has previously included the .itp files http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File for that force field. Appropriate use of the |#define| and |#ifdef| mechanisms can permit the same .itp file http://www.gromacs.org/** Documentation/File_Formats/.**itp_Filehttp://www.gromacs.org/Documentation/File_Formats/.itp_File to work with multiple force fields, e.g. |share/top/water.itp|. Note the key caveat here - through the use of #define and #ifdef you can make use of different force fields. That means you can control which parameters are applied based on different conditions. I could write an .itp file for any molecule that has force field parameters for any force field, and all I'd have to do is enclose all relevant directives within #ifdef blocks and it would work. This note does *not* indicate that you can mix and match force fields. Doing so is generally a very bad idea, if it even works syntactically. so, i think even though the swissparam generated topologies based on MMFF fit to charmm (based on testing), they could also be used
Re: [gmx-users] mktop
Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. While searching for the literature on compatibility of lipid FF and protein FF, I found few references where similar modification was done for DOPC lipid bilayer and were suitable with various FF for proteins and also with CHARMM FF: 1. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields.J Comput Chem 32: 1400–1410, 2011. I don't have the lipid bilayer with their itp files with CHARMM FF parameterization. Please could you inform me where to obtain them, so that i can use the lipid bilayer structure for embedding the protein and use the related CHARMM FF parameterised itp in the topology file in gromacs for MD simulation. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks, and I accept your suggestions; If SwissParam was designed to be used with CHARMM, the most intuitive next step is to use CHARMM for the MD, is it not?I understand the point about trying to keep the force fields consistent between docking and MD, but it may not be feasible (i.e., there may not be suitable parameters in OPLS for the bizarre functional groups you're dealing with). Yes, I also tried CHARMM FF to generate the topology file of the protein using pdb2gmx (without ligand), and as per the swissparam and gromacs tutorial i could build the protein-ligand-lipid bilayer and minimize it using mdrun and and i am at the NPT equilibration step, everything is ok with this procedure and without errors, but my lipid bilayer is made up of POPC and the POPC itp file has OPLS FF topologies. So, i was wondering whether the POPC itp file i am using for MD simulations can be used with the protein and ligand topology file generated by CHARMM. You shouldn't mix and match force fields. Suitable CHARMM lipid parameters are widely available. and as per the swissparam tutorial the command to generate topology file for protein is: pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp in the gromacs 4.5.4 version the option to select Charmm FF from the pdb2gmx command is available, but i could not understand the usage of -nochargegp flag as per the tutorial, is this flag still valid while generating toplogies. CHARMM does not use charge groups. Therefore, each atom should be its own group in the topology. Using -nochargegrp overrides the default behavior of the .rtp files (which has multi-atom charge groups, although I think this was changed somewhere along the way, but I don't remember if it was before or after 4.5.4). -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/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] make_ndx unable to save
Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containing the new groups, but while creating the new index file I could select groups , but unable to save them using 'q' command. jhcdyprod31ns.gro is the output file after simulation for a period of time. I executed the command: make_ndx -f jhcdyprod31ns.gro -o output.ndx * then i got the following options,* Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 539Protein residues There are: 5Ion residues There are: 133 Other residues There are: 15828 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 62876 atoms 1 Protein : 8470 atoms 2 Protein-H : 4235 atoms 3 C-alpha : 539 atoms 4 Backbone: 1617 atoms 5 MainChain : 2157 atoms 6 MainChain+Cb: 2652 atoms 7 MainChain+H : 2675 atoms 8 SideChain : 5795 atoms 9 SideChain-H : 2078 atoms 10 Prot-Masses : 8470 atoms 11 non-Protein : 54406 atoms 12 Ion : 5 atoms 13 NA : 2 atoms 14 CL : 1 atoms 15 LIG :53 atoms 16 POPC: 6864 atoms 17 CL- : 2 atoms 18 Other : 6917 atoms 19 NA : 2 atoms 20 CL : 1 atoms 21 LIG :53 atoms 22 POPC: 6864 atoms 23 CL- : 2 atoms 24 Water : 47484 atoms 25 SOL : 47484 atoms 26 non-Water : 15392 atoms 27 Water_and_ions : 47489 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index * but, i wanted to create a new group, so i selected a residue number 15 and verified it as a new group added in the index file, this was ok * r15 28 r_15:12 atoms* 0 System : 62876 atoms 1 Protein : 8470 atoms 2 Protein-H : 4235 atoms 3 C-alpha : 539 atoms 4 Backbone: 1617 atoms 5 MainChain : 2157 atoms 6 MainChain+Cb: 2652 atoms 7 MainChain+H : 2675 atoms 8 SideChain : 5795 atoms 9 SideChain-H : 2078 atoms 10 Prot-Masses : 8470 atoms 11 non-Protein : 54406 atoms 12 Ion : 5 atoms 13 NA : 2 atoms 14 CL : 1 atoms 15 LIG :53 atoms 16 POPC: 6864 atoms 17 CL- : 2 atoms 18 Other : 6917 atoms 19 NA : 2 atoms 20 CL : 1 atoms 21 LIG :53 atoms 22 POPC: 6864 atoms 23 CL- : 2 atoms 24 Water : 47484 atoms 25 SOL : 47484 atoms 26 non-Water : 15392 atoms 27 Water_and_ions : 47489 atoms 28 r_15:12 atoms then**, i save it with q command * q Back Off! I just backed up output.ndx to ./#output.ndx.15# but, when i wanted to add another group to this index file i again i could not see the first new group added i.e. it has the default groups, the new groups added are not saved. Please let know your suggestions to overcome this error. Thanks, ram * * -- 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] RHEL OS, g_mdrun
Dear Justin, Thanks for the suggestion. Do we need to install FFTW libraries also while installing gromacs as I think FFT pack got installed as default when the gromacs is installed by the system admin using yum i.e. yum install gromacs. yum install gromacs_openmpi / yum install gromacs_mpich2, because when i asked my system administrator he mentioned that he installed mpich2 version of gromacs, but when i tried to locate g_mdrun_mpich2, i could not find it in the path, instead i found g_mdrun_openmpi and so i tried to run the job with g_mdrun_openmpi, but could not run the job. So it is difficult now to figure out why I could not use g_mdrun_openmpi, even though the file exists in the path:/usr/lib64/openmpi/bin/g_mdrun_openmpi Ram On Wed, May 18, 2011 at 3:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am trying to run a gromacs mdrun job (pbs script) on the cluster (RHEL operating system) using the recently installed gromacs version 4.5.3, but i think i could not run it paralleled on the nodes, as it is taking a long time to finish the job. The information regarding the installed gromacs on the server is as follows: Scheduler: Moab/Torque Mpi Version: Mpich2 OS: RHEL 5.5 Compiler: gcc version 4.4 enterprise linux 5 FFT – FFT Pack I am running a batch job using the script as under: #PBS -S /bin/bash #PBS -N aarontest #PBS -o aaronout.txt #PBS -j oe #PBS -l nodes=2:ppn=4 #PBS -l walltime=336:00:00 #cat $PBS_NODEFILE NP=`wc -l $PBS_NODEFILE` cd $PBS_O_WORKDIR #export MPI_GROUP_MAX=128 /usr/local/bin/mpirun -np 8 /usr/bin/g_mdrun -nt 8 -deffnm testnpt3ns -v dlb yes -rdd 1.2 Please let me know your suggestions for correcting the error. MPI and threading are mutually exclusive; you can't launch a multi-thread process (mdrun -nt) via mpirun. The mdrun executable must be MPI-enabled to run on this system. Perhaps the pre-compiled binary is not, in which case you should install from source with --enable-mpi and --disable-threads. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] protein movement in lipid bilayer during simulation
Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see that the protein started moving in one dimension in the lipid bilayer that is it is not in the centre, I want the position of the protein fixed through out the simulation, so pl suggest regarding this.. and is it ok if I increase the position restraints for the protein by changing the values of forces on x y and z dimensions in the posre.itp file (below) of the protein, and if so how much can i increase the force, so that i doesnot effect the simulation. [ position_restraints ] ; atom type fx fy fz 1 1 2000 2000 2000 5 1 2000 2000 2000 7 1 2000 2000 2000 10 1 2000 2000 2000 13 1 2000 2000 2000 14 1 2000 2000 2000 18 1 2000 2000 2000 19 1 2000 2000 2000 20 1 2000 2000 2000 21 1 2000 2000 2000 23 1 2000 2000 2000 26 1 2000 2000 2000 29 1 2000 2000 2000 32 1 2000 2000 2000 33 1 2000 2000 2000 34 1 2000 2000 2000 35 1 2000 2000 2000 37 1 2000 2000 2000 40 1 2000 2000 2000 Thanks in advance, Ram -- 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] protein movement in lipid bilayer during simulation
Dear Justin, Thanks for the suggestion. Best, Ram On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see that the protein started moving in one dimension in the lipid bilayer that is it is not in the centre, I want the position of the protein fixed through out the simulation, so pl suggest regarding this.. This is a normal consequence of diffusion in a periodic system. There is no such thing as a center. For visualization purposes, just post-process your trajectory with trjconv. and is it ok if I increase the position restraints for the protein by changing the values of forces on x y and z dimensions in the posre.itp file (below) of the protein, and if so how much can i increase the force, so that i doesnot effect the simulation. If you're trying to get around the diffusion issue, don't. If this is part of equilibration, all you're doing is setting up a higher energy barrier for the movement of these atoms. The difference between 1000 and 2000 should be relatively minimal, as far as the end result is concerned. -Justin [ position_restraints ] ; atom type fx fy fz 1 1 2000 2000 2000 5 1 2000 2000 2000 7 1 2000 2000 2000 10 1 2000 2000 2000 13 1 2000 2000 2000 14 1 2000 2000 2000 18 1 2000 2000 2000 19 1 2000 2000 2000 20 1 2000 2000 2000 21 1 2000 2000 2000 23 1 2000 2000 2000 26 1 2000 2000 2000 29 1 2000 2000 2000 32 1 2000 2000 2000 33 1 2000 2000 2000 34 1 2000 2000 2000 35 1 2000 2000 2000 37 1 2000 2000 2000 40 1 2000 2000 2000 Thanks in advance, Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] cannot rename checkpoint file
Dear Gromacs users, I am running an all-atom simulation of protein-ligand complex in lipid bilayer on a server, while running the job after some time, my job terminates with an error as under: Program mdrun, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error: Cannot rename checkpoint file; maybe you are out of quota? Please suggest how to overcome this error. Best, Ram -- 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] tpbconv extension
Dear Gromacs users, I -- 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: tpbconv extension
Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: tpbconv extension
Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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] Re: tpbconv extension
Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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] Re: tpbconv extension
Hi Berk, Thanks for the suggestion, does the tpr file generated by the options mention on PC would work on a server with older version of Gromacs i.e. 4.0... Ram On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess g...@hotmail.com wrote: Sorry, I mistook a million ps for a millisecond, this is a microsecond. The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647. From the name of your tpr file it seems you are not exceeding this, so I don't know what's wrong exactly. But for this reason (and many other reasons), you might want to consider upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before). Berk Date: Mon, 13 Dec 2010 17:56:43 +0100 Subject: Re: [gmx-users] Re: tpbconv extension From: rmbio...@gmail.com To: jalem...@vt.edu; gmx-users@gromacs.org CC: Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead. There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem. I believe all of this has been resolved as of Gromacs 4.5, for future reference. -Justin Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not writing tpr file Please give your suggestions to overcome this error. What was your command? -Justin Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-us...@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] swiss param query,
Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for tpr generation I am getting an error as follows: Atomtype C5A not found Please let me know your suggestions, to correct this error, I have included ligand.itp in the topology file of the protein. Thanks, ram grompp -f mdions.mdp -c combi.gro -p topol.top -o combi.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# checking input for internal consistency... NOTE 1 [file mdions.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ffoplsaabon.itp Generated 348195 of the 348195 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 348005 of the 348195 1-4 parameter combinations Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/tip3p.itp Opening library file /usr/local/gromacs-4.0.7-single/share/gromacs/top/ions.itp --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 947 Fatal error: Atomtype C5A not found -- 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] trjcat : Magic Number Error in XTC file (read 0, should be 1995)
Subject: trjcat : Magic Number Error in XTC file (read 0, should be 1995) Dear Gromacs Users, I am trying to cat the .xtc files using the trjcat option in gromacs, but i am getting an error Program gmxcheck, VERSION 4.0.7 Source code file: xtcio.c, line: 85 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) when i execute this command. Please provide your suggestions to overcome this error.. Thanks, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] inversion of lipid bilayer with water in the centre
Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... Thanks Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coarse grain dynamics
thanks all for the discussion. On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... There are tools out there to reconstruct an atomistic representation of a CG system (see link below, and poke around Google for a few minutes). If you want to start a whole new simulation, that is certainly possible after (of course) regenerating your system topology to match the new system. -Justin On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson thomp...@purdue.edu wrote: I agree with Justin on this one. Simulations run using CG that is not optimized for reconstruction may not actually reflect the type of interactions you are looking for. The current result of this simulation may not directly correspond to a full atomistic result, so even if a reconstruction were performed you would most likely NOT be able to draw conclusions from it. Otherwise, everyone would run really fast simulations in CG, then reconstruct their systems afterward. :) Quoting Justin A. Lemkul jalem...@vt.edu: ram bio wrote: thanks, but i am using gromacs version 4.0.07 I think the general consensus thus far is you won't be able to do what you want without significant effort to reconstruct your system, and perhaps then you should question whether any tools that seek to build optimal hydrogens from CG structures are going to bias the result. Would those hydrogen bonds have actually formed in an AA simulation? Hard to tell. If you want to analyze hydrogen bonds, CG approximations are not probably sufficient. This is a good exercise in planning your analysis before conducting your simulation. You can probably estimate some sort of polar contacts from your CG representation, but not hydrogen bonds. -Justin On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi egv...@gmail.com wrote: Hi, To change between representations (atomistic -- coarse grained), if you are using the MARTINI FF, you can use the modified version of Gromacs 3.3, check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt If you don't want to switch to full-atomistic representation, check which CG atom types are able to form hydrogen bonds and look for interactions between them. Obviously, this will be an approximation. Esteban G. Vega-Hissi UNSL San Luis Argentina -- On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson thomp...@purdue.edu wrote: There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia naz...@det.uminho.pt: Hi there! I never worked with coarse grain simulations, but if you used a coarse grain methodology you didn't include all the atoms, so you didn't included hydrogens. So now you can not see them, of course. They are not there. If you need to know the hydrogen bond interactions you need to do some all atoms simulation, not coarse grain. Nuno Azoia On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bonding distance and the hydrogen bonds existing.. Thanks Ram -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt http://nazoia.net -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users
[gmx-users] coarse grain dynamics
Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bonding distance and the hydrogen bonds existing.. Thanks Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coarse grain dynamics
thanks, but i am using gromacs version 4.0.07 On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi egv...@gmail.com wrote: Hi, To change between representations (atomistic -- coarse grained), if you are using the MARTINI FF, you can use the modified version of Gromacs 3.3, check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt If you don't want to switch to full-atomistic representation, check which CG atom types are able to form hydrogen bonds and look for interactions between them. Obviously, this will be an approximation. Esteban G. Vega-Hissi UNSL San Luis Argentina -- On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson thomp...@purdue.edu wrote: There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia naz...@det.uminho.pt: Hi there! I never worked with coarse grain simulations, but if you used a coarse grain methodology you didn't include all the atoms, so you didn't included hydrogens. So now you can not see them, of course. They are not there. If you need to know the hydrogen bond interactions you need to do some all atoms simulation, not coarse grain. Nuno Azoia On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bonding distance and the hydrogen bonds existing.. Thanks Ram -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt http://nazoia.net -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coarse grain dynamics
Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson thomp...@purdue.edu wrote: I agree with Justin on this one. Simulations run using CG that is not optimized for reconstruction may not actually reflect the type of interactions you are looking for. The current result of this simulation may not directly correspond to a full atomistic result, so even if a reconstruction were performed you would most likely NOT be able to draw conclusions from it. Otherwise, everyone would run really fast simulations in CG, then reconstruct their systems afterward. :) Quoting Justin A. Lemkul jalem...@vt.edu: ram bio wrote: thanks, but i am using gromacs version 4.0.07 I think the general consensus thus far is you won't be able to do what you want without significant effort to reconstruct your system, and perhaps then you should question whether any tools that seek to build optimal hydrogens from CG structures are going to bias the result. Would those hydrogen bonds have actually formed in an AA simulation? Hard to tell. If you want to analyze hydrogen bonds, CG approximations are not probably sufficient. This is a good exercise in planning your analysis before conducting your simulation. You can probably estimate some sort of polar contacts from your CG representation, but not hydrogen bonds. -Justin On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi egv...@gmail.com wrote: Hi, To change between representations (atomistic -- coarse grained), if you are using the MARTINI FF, you can use the modified version of Gromacs 3.3, check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt If you don't want to switch to full-atomistic representation, check which CG atom types are able to form hydrogen bonds and look for interactions between them. Obviously, this will be an approximation. Esteban G. Vega-Hissi UNSL San Luis Argentina -- On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson thomp...@purdue.edu wrote: There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia naz...@det.uminho.pt: Hi there! I never worked with coarse grain simulations, but if you used a coarse grain methodology you didn't include all the atoms, so you didn't included hydrogens. So now you can not see them, of course. They are not there. If you need to know the hydrogen bond interactions you need to do some all atoms simulation, not coarse grain. Nuno Azoia On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bonding distance and the hydrogen bonds existing.. Thanks Ram -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt http://nazoia.net -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion of desmond trajectory files into gromacs
Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Multiprotein lipid bilayer
Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please let me know if any tutorial is available or any kind of help is available Thanks in advance, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Multiprotein lipid bilayer
HI Justin, Thanks for the info. I have followed your tutorial earlier, it really works, and that was for 1 protein, but if 2 or more different kinds of proteins are to be inserted then how to generate the a single topology file for all the proteins using pdb2gmx and also can you please let me know the other ways to insert the proteins in lipid bilayers Ram On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please Just about anything is possible :) let me know if any tutorial is available or any kind of help is available There is a tutorial for a basic membrane protein system linked from the Gromacs tutorials page. As for inserting multiple proteins in the membrane, there are several ways to do it, but if you want to use InflateGRO, you'll need the latest version: http://www.csb.bit.uni-bonn.de/inflategro.html -Justin Thanks in advance, Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Multiprotein lipid bilayer
hi justin, will try that thanks Ram On Thu, Mar 4, 2010 at 4:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: HI Justin, Thanks for the info. I have followed your tutorial earlier, it really works, and that was for 1 protein, but if 2 or more different kinds of proteins are to be inserted then how to generate the a single topology file for all the proteins using pdb2gmx and also can you please let me know the other ways to insert the proteins in lipid bilayers You don't need a single topology for all the proteins. Instead you can generate individual topologies for each protein with pdb2gmx, remove the unnecessary #includes, [system], and [molecules] directives to make them single-molecule .itp files, and then simply: #include protein_A.itp #include protein_B.itp in your .top file. Other ways to insert proteins might include using genbox creatively, VMD, g_membed, etc. Search the list archive. -Justin Ram On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please Just about anything is possible :) let me know if any tutorial is available or any kind of help is available There is a tutorial for a basic membrane protein system linked from the Gromacs tutorials page. As for inserting multiple proteins in the membrane, there are several ways to do it, but if you want to use InflateGRO, you'll need the latest version: http://www.csb.bit.uni-bonn.de/inflategro.html -Justin Thanks in advance, Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp segmentation error
Dear Justin, I am having grompp segmentation error only for the drug-enzyme complex tutorial, all other executables are ok, can this occur due to the any other reasons like following the tutorial improperly. Thanks, Ram On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Does grompp give any other output, or does it just seg fault? Do other executables work on this system? There are a whole host of issues that could be causing this, from 32/64 bit mismatch, shared libraries being moved, etc, so it is very difficult to diagnose. Was the whole package compiled with MPI (per the above command)? If so, there is no point, since the only MPI-enabled executable is mdrun. It may help to re-compile correctly if this is the case (a bit of a long shot, but perhaps worth trying). Do you have gcc available on the cluster, to test and see if it produces functioning code? -Justin Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the response. I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have asked my system admin to provide the details regarding the cluster, whereas for my PC: The info is as follows: 1. The Gromacs version you are using. - 4.0.3 2. The compilers used in installing Gromacs.- gcc gcc -v Using built-in specs. Target: i386-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=i386-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs source code download site: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. I would suggest updating to the latest version of Gromacs (4.0.7), using a more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and 4.2.x and newer, are fine). 3. Options specified during configuration. I didnot get this, can you please elaborate... Things like --enable-shared, --disable-(whatever), but I don't know that any of this is relevant. I think the compiler is the problem. -Justin 4. Specifications of your hardware. processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 13 model name : Intel(R) Pentium(R) M processor 1.70GHz stepping : 6 cpu MHz : 600.000 cache size : 2048 KB fdiv_bug : no hlt_bug : no f00f_bug : no coma_bug : no fpu : yes fpu_exception : yes cpuid level : 2 wp : yes flags : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2 bogomips : 1196.53 Linux version 2.6.18-8.el5 (mockbu...@builder4.centos.org) (gcc version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35 EDT 2007 Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc. Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Thu Mar 15 19:57:35 EDT 2007 i686 Build Date: 21 June 2008 Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1 I would be providing the info about the cluster, once I receive it, mean please let me know if any info is missing and help me. Thanks, Ram On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr :-) grompp (-: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/local/gromacs/share
Re: [gmx-users] grompp segmentation error
Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers. $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s = Linux uname -v = #1 SMP Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the response. I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have asked my system admin to provide the details regarding the cluster, whereas for my PC: The info is as follows: 1. The Gromacs version you are using. - 4.0.3 2. The compilers used in installing Gromacs.- gcc gcc -v Using built-in specs. Target: i386-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=i386-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) The gcc 4.1.x is well-known to be buggy, and as advised on the Gromacs source code download site: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. I would suggest updating to the latest version of Gromacs (4.0.7), using a more reliable compiler (other versions of gcc, i.e. 4.0.x and older, and 4.2.x and newer, are fine). 3. Options specified during configuration. I didnot get this, can you please elaborate... Things like --enable-shared, --disable-(whatever), but I don't know that any of this is relevant. I think the compiler is the problem. -Justin 4. Specifications of your hardware. processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 13 model name : Intel(R) Pentium(R) M processor 1.70GHz stepping: 6 cpu MHz : 600.000 cache size : 2048 KB fdiv_bug: no hlt_bug : no f00f_bug: no coma_bug: no fpu : yes fpu_exception : yes cpuid level : 2 wp : yes flags : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2 bogomips: 1196.53 Linux version 2.6.18-8.el5 (mockbu...@builder4.centos.org) (gcc version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35 EDT 2007 Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc. Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Thu Mar 15 19:57:35 EDT 2007 i686 Build Date: 21 June 2008 Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1 I would be providing the info about the cluster, once I receive it, mean please let me know if any info is missing and help me. Thanks, Ram On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr :-) grompp (-: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Segmentation fault what i have done is as per the tutorial, that is 1) generated the drg.itp using prodrug beta 2) executed pdb2gmx using 4 that is ff53a6 ff 3) edit the drg.itp by removing the lines redundant as per trp.top 4) edit trp.gro by adding drg coordinates and chainging the numbers please help me to overcome this error, for your convenience I have attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files. I doubt any of these files will be useful. Better information would include: 1. The Gromacs version you are using. 2. The compilers used in installing Gromacs. 3. Options specified during configuration. 4. Specifications of your hardware. A segmentation fault is a memory error and can have numerous causes. The above information may be useful. -Justin Thanks, Ram 4 attachments
Re: [gmx-users] grompp segmentation error
Dear Justin, Thanks for the response. I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have asked my system admin to provide the details regarding the cluster, whereas for my PC: The info is as follows: 1. The Gromacs version you are using. - 4.0.3 2. The compilers used in installing Gromacs.- gcc gcc -v Using built-in specs. Target: i386-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=i386-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-44) 3. Options specified during configuration. I didnot get this, can you please elaborate... 4. Specifications of your hardware. processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 13 model name : Intel(R) Pentium(R) M processor 1.70GHz stepping: 6 cpu MHz : 600.000 cache size : 2048 KB fdiv_bug: no hlt_bug : no f00f_bug: no coma_bug: no fpu : yes fpu_exception : yes cpuid level : 2 wp : yes flags : fpu vme de pse tsc msr mce cx8 mtrr pge mca cmov pat clflush dts acpi mmx fxsr sse sse2 ss tm pbe up est tm2 bogomips: 1196.53 Linux version 2.6.18-8.el5 (mockbu...@builder4.centos.org) (gcc version 4.1.1 20070105 (Red Hat 4.1.1-52)) #1 SMP Thu Mar 15 19:57:35 EDT 2007 Build Operating System: Linux 2.6.18-53.1.14.el5PAE i686 Red Hat, Inc. Current Operating System: Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Thu Mar 15 19:57:35 EDT 2007 i686 Build Date: 21 June 2008 Build ID: xorg-x11-server 1.1.1-48.41.el5_2.1 I would be providing the info about the cluster, once I receive it, mean please let me know if any info is missing and help me. Thanks, Ram On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr :-) grompp (-: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Segmentation fault what i have done is as per the tutorial, that is 1) generated the drg.itp using prodrug beta 2) executed pdb2gmx using 4 that is ff53a6 ff 3) edit the drg.itp by removing the lines redundant as per trp.top 4) edit trp.gro by adding drg coordinates and chainging the numbers please help me to overcome this error, for your convenience I have attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files. I doubt any of these files will be useful. Better information would include: 1. The Gromacs version you are using. 2. The compilers used in installing Gromacs. 3. Options specified during configuration. 4. Specifications of your hardware. A segmentation fault is a memory error and can have numerous causes. The above information may be useful. -Justin Thanks, Ram 4 attachments — -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp segmentation error
Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr :-) grompp (-: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Segmentation fault what i have done is as per the tutorial, that is 1) generated the drg.itp using prodrug beta 2) executed pdb2gmx using 4 that is ff53a6 ff 3) edit the drg.itp by removing the lines redundant as per trp.top 4) edit trp.gro by adding drg coordinates and chainging the numbers please help me to overcome this error, for your convenience I have attached the drg.itp, trp.top, trp.gro and trp_b4ion.gro files. Thanks, Ram 4 attachments — -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Truncation of file traj.trr failed
Dear Justin, As per the suggestions in the bug, i changed the line in src/gmxlib/checkpoint.c file on the cluster: from outputfiles[i].offset = ( ((off_t) offset_high) 32 )| ( (off_t) offset_low ); to outputfiles[i].offset = ( ((off_t) offset_high) 32 )| ( (off_t) offset_low mask ); and was able to use the -append option, my command was mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append and this run generated another 3ns production data (from the step 2928600 - 590) and thus increasing the size of trr file to 4.8 GB from 2.1 GB, because my simulation is for 20ns, i submitted one more job with the same command after completing the 5.9 ns, mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append now again the job is starting from same step 2928600, i also tried using the command mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state_prev.cpt -append here also the output is same that is starting from 2928600 step, i want to continue the run from 590 step, please let me know how to proceed, do i have to generate a new .tpr file (my mdp file is defined for 20 ns and the output is md20.tpr) or can i use the same tpr file (md20.tpr) or i require to change the command to continue.. Please help. Thanks, Ram On Fri, Nov 6, 2009 at 10:15 PM, ram bio rmbio...@gmail.com wrote: Dear Justin, Thanks for the information regarding the bug, will try the solutions in the site. Ram On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a protein-lipid bilayer simulation for 20ns. I am using Gromacs version 4.0.5 and when i want to continue the mdrun using -append command , I am getting an error as follows: Getting Loaded... Reading file md20.tpr, VERSION 4.0.5 (single precision) Reading checkpoint file state.cpt generated: Fri Nov 6 15:22:25 2009 --- Program mdrun, VERSION 4.0.5 Source code file: checkpoint.c, line: 1248 Fatal error: Truncation of file traj.trr failed. Please suugest me how to overcome this error and continue the mdrun. http://bugzilla.gromacs.org/show_bug.cgi?id=341 I believe this bug has been fixed in the development version (available through git). -Justin Thanks, Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Truncation of file traj.trr failed
Dear justin, The job was terminated as under: vol 0.92 imb F 1% step 5860300, will finish Sun Nov 15 06:56:32 2009 = PBS: job killed: walltime 86438 exceeded limit 86400 mpiexec: killing job... i think due to queueing system and maximum time being 24hrs. i donot know how to know whether new cpt files are written all the files i have are the same 2 cpt files state.cpt and state_prev.cpt. when i did gmxcheck on both cpt files the output was Checking file state.cpt # Atoms 31609 Last frame -1 time 2928.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 for state_prev.cpt # Atoms 31609 Last frame -1 time 2896.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 when the run is extended for the second time do gromacs generate a new cpt file i mean with new name or same named files (state.cpt and state_prev.cpt) with new check points written.. Please help Thanks, Ram On Tue, Nov 10, 2009 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As per the suggestions in the bug, i changed the line in src/gmxlib/checkpoint.c file on the cluster: from outputfiles[i].offset = ( ((off_t) offset_high) 32 )| ( (off_t) offset_low ); to outputfiles[i].offset = ( ((off_t) offset_high) 32 )| ( (off_t) offset_low mask ); and was able to use the -append option, my command was mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append and this run generated another 3ns production data (from the step 2928600 - 590) and thus increasing the size of trr file to 4.8 GB from 2.1 GB, because my simulation is for 20ns, i submitted one more job with the same command after completing the 5.9 ns, So the job crashed again, then? mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append now again the job is starting from same step 2928600, i also tried using the command mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state_prev.cpt -append here also the output is same that is starting from 2928600 step, i want to continue the run from 590 step, please let me know how to proceed, do i have to generate a new .tpr file (my mdp file is defined for 20 ns and the output is md20.tpr) or can i use the same tpr file (md20.tpr) or i require to change the command to continue.. Were new .cpt files actually written? What does gmxcheck tell you about each of them? It would seem that the simulation did not run long enough for new .cpt files to be generated, or there was otherwise some problem with writing the new file. You should not need a new .tpr file if you have not yet completed the required 20 ns. See here: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin Please help. Thanks, Ram On Fri, Nov 6, 2009 at 10:15 PM, ram bio rmbio...@gmail.com wrote: Dear Justin, Thanks for the information regarding the bug, will try the solutions in the site. Ram On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a protein-lipid bilayer simulation for 20ns. I am using Gromacs version 4.0.5 and when i want to continue the mdrun using -append command , I am getting an error as follows: Getting Loaded... Reading file md20.tpr, VERSION 4.0.5 (single precision) Reading checkpoint file state.cpt generated: Fri Nov 6 15:22:25 2009 --- Program mdrun, VERSION 4.0.5 Source code file: checkpoint.c, line: 1248 Fatal error: Truncation of file traj.trr failed. Please suugest me how to overcome this error and continue the mdrun. http://bugzilla.gromacs.org/show_bug.cgi?id=341 I believe this bug has been fixed in the development version (available through git). -Justin Thanks, Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, Thanks for your patience and suggestions, as I am new to gromacs, i had to confirm my results. Ram On Mon, Oct 26, 2009 at 4:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As per the suggestions, I have run NPT equillibration (without constraints) for 1ns and observed the average values and plots in the xmgrace as follows: 1) Pressure Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 0.967068315.557315.557 -0.00139934 -1.39934 In the pressure.xvg plot the pressure was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 2) Density Energy Average RMSD Fluct. Drift Tot-Drift --- Density (SI)1010.056.139124.17568 0.0155894 15.5894 In the density.xvg plot the density in the beginning was around 984 and then increased upto 500 ps then onwards was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 3) temperature Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 3231.689791.68965 7.75704e-05 0.0775705 Heat Capacity Cv: 12.4723 J/mol K (factor = 2.73692e-05) In the temperature.xvg plot the pressure was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 4) Box-x Statistics over 101 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Box-X 6.81637 0.00919707 0.00692067 -2.09829e-05 -0.0209829 In the box-x.xvg plot the value decreased from 6.82 - 6.84 to 6.79 - 6.81 after the 500 ps and then was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 5) Box-Y the trend was same as X dimension Energy Average RMSD Fluct. Drift Tot-Drift --- Box-Y 6.84395 0.00923428 0.00694867 -2.10678e-05 -0.0210678 5) Box-Z the trend was same as X dimension Statistics over 101 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Box-Z9.0932 0.0438719 0.036307 -8.53145e-05 -0.0853146 In the box-z.xvg plot the value started from 9.3 and decreased to 9.03 at the 500 ps and then the values were fluctuating around this value in the same run. Please suggest me are my equilibrated parameters ok for the MD production run or i have to look for some more parameters and is it ok if i run the production phase also without constraints and position restraints. You've presented six pieces of data that have all stabilized. You have to make the decision as to whether or not your equilibration is sufficient; you can't rely on others who know nothing about your project or its goals to continually check it and tell you if it's right. -Justin The mdp file used for NPT is as below: title = NPT Equilibration define = -DPOSRES integrator = md nsteps = 100 dt = 0.001 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation= yes constraint_algorithm = lincs constraints = none lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- Thanks, Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, As per the suggestions, I have run NPT equillibration (without constraints) for 1ns and observed the average values and plots in the xmgrace as follows: 1) Pressure Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 0.967068315.557315.557 -0.00139934 -1.39934 In the pressure.xvg plot the pressure was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 2) Density Energy Average RMSD Fluct. Drift Tot-Drift --- Density (SI)1010.056.139124.17568 0.015589415.5894 In the density.xvg plot the density in the beginning was around 984 and then increased upto 500 ps then onwards was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 3) temperature Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 3231.689791.68965 7.75704e-05 0.0775705 Heat Capacity Cv: 12.4723 J/mol K (factor = 2.73692e-05) In the temperature.xvg plot the pressure was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 4) Box-x Statistics over 101 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Box-X 6.81637 0.00919707 0.00692067 -2.09829e-05 -0.0209829 In the box-x.xvg plot the value decreased from 6.82 - 6.84 to 6.79 - 6.81 after the 500 ps and then was the same through out the equilibration, that is no rise or fall in the graph, fluctuating in the same range. 5) Box-Y the trend was same as X dimension Energy Average RMSD Fluct. Drift Tot-Drift --- Box-Y 6.84395 0.00923428 0.00694867 -2.10678e-05 -0.0210678 5) Box-Z the trend was same as X dimension Statistics over 101 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 101 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Box-Z9.0932 0.0438719 0.036307 -8.53145e-05 -0.0853146 In the box-z.xvg plot the value started from 9.3 and decreased to 9.03 at the 500 ps and then the values were fluctuating around this value in the same run. Please suggest me are my equilibrated parameters ok for the MD production run or i have to look for some more parameters and is it ok if i run the production phase also without constraints and position restraints. The mdp file used for NPT is as below: title = NPT Equilibration define = -DPOSRES integrator = md nsteps = 100 dt = 0.001 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation= yes constraint_algorithm = lincs constraints = none lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- Thanks, Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift
Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking
Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me. Thanks, Ram On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, That's all very well, but what will that give you other than a set where the partition of total energy into potential and kinetic was skewed one way? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking
Dear Mark, Thanks and you are right, that when a docked complex (protein + ligand) is simulated, the favorable ligand binding poses can be predicted using MD (longer runs). What I am trying to do here presently is not to simulate a docked complex, but to generate a modelled protein lowest energy configuration (P.E. surface exploration) using MD and further use this configuration for the flexible docking, and you are right as I think MD follows the law of conservation of energy as the P.E decreases the K.E increases or vice versa for a configuration at an instance, as we are exploring the P.E surface by changing the coordinates very effectively using M.D, i want use the configuration (coordinates) with the lowest P.E produced from MD and further minimize it (as i dont know whether the configuration obtained after gromacs MD can go further into a local/global minima by minimization) so that can be the input for flexible docking. Thanks, Ram On Thu, Oct 22, 2009 at 4:59 PM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me. If you read your docking program's documentation, they are using their energy as a some kind of approximation to a free energy of ligand binding (or some such). There could be all kinds of ad-hoc contributions that they may have been able to demonstrate worked usefully enough on their test set to be worth including. There's no reason to assume an MD potential energy (which itself is a combination of more-or-less ad-hoc parameters) would correlate with the above, since the MD potential wasn't parameterized to do that. It'd be especially flawed to suppose that the fact that energy in MD is distributed over PE and KE is immaterial. Low PE just means high KE. To identify favourable ligand-binding orientations with MD requires an immense amount of sampling. In effect, you need to do enough MD to allow the ligand to come in and out of the site many times in many different ways and to compare the relative frequency so that you can also estimate the entropy component of the free energy change associated with various binding modes relative to each other. Even for implicit solvent calculation models, the history of computing probably doesn't provide enough cycles to do this with decent accuracy. Hence, docking. MD can be useful in more limited docking studies - a highly unfavourable binding conformation will fly apart rapidly - but you'd hope the docking force field could tell you about those cases! It sounds like you should really be doing some more background reading about docking and MD, to better understand the methods you're using. Mark On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, That's all very well, but what will that give you other than a set where the partition of total energy into potential and kinetic was skewed one way? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Protein Solvent Dynamics - Coordinates for docking
Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial. Can anybody tell me how to extract the coordinates ? of the simulated protein (file after extraction ?) and is it necessary to minimize the simulated protein in vacco to use it for further docking studies. Please help. Thanks, ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking
Dear Mark, Thanks for the advice and suggestions. I have used trjconv command as in the justin tutorial (trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact), but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD, i could not see the protein jumping out of the box on one side. I am doing something wrong, Please let me know, and was able to calculate rmsd plot as per the command: g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns and i want convert the coordinates of the simulated protein in pdb format, and as I learnt that the coordinates are written in .trr or .xtc file and i also have a md_0_1.gro file, so can i use editconf -f md_0_1.gro -o md_0_1.pdb command to convert the coordinates of the simulated protein into PDB format,is it ok.. or else should i use trjconv -f md_0_1.xtc -o md_0_1.pdb.Please suggest me the correct script. Regarding docking when I did solvent simulation on GUI commercial software, I used to minimize the simulated structure for docking, but i have no clues learnt in gromacs tutorial ( iam new to gromacs) regarding the output whether it is minimized after simulation or not the md.mdp file which i used for the production MD is as below: title = MD integrator = md nsteps = 50 dt = 0.002 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 pbc = xyz DispCorr= EnerPres gen_vel = no Thanks, Ram On Wed, Oct 21, 2009 at 4:42 PM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial. Can anybody tell me how to extract the coordinates ? of the simulated protein (file after extraction ?) and is it necessary to minimize the It sounds like you should be doing more tutorials to understand GROMACS workflows better. What coordinates you produced are in the .trr or .xtc files, but what data is there with what frequency is set up in your .mdp file, so you need to plan that in advance. trjconv is the tool for manipulating those files, for example to extract frames as PDB to use with some other software. simulated protein in vacco to use it for further docking studies. Maybe. Read the docking literature, or do some tutorials there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking
Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, i want to collect the structure (coordinates in pdb) representing average of all the frames/configurations produced in MD and also the lowest energy configuration structure (coordinates in PDB) produced during the simulation, which can be used for docking. Please help how to obtain the average structure as well as the lowest energy configuration structure. Thanks, Ram On Wed, Oct 21, 2009 at 6:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Mark, Thanks for the advice and suggestions. I have used trjconv command as in the justin tutorial (trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact), but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD, i could not see the protein jumping out of the box on one side. I am doing something wrong, Please let me know, and was able to calculate rmsd plot as per the command: g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns If you don't see the protein jumping, then what's the problem? That's the point of using trjconv - to correct periodicity. and i want convert the coordinates of the simulated protein in pdb format, and as I learnt that the coordinates are written in .trr or .xtc file and i also have a md_0_1.gro file, so can i use editconf -f md_0_1.gro -o md_0_1.pdb command to convert the coordinates of the simulated protein into PDB format,is it ok.. or else should i use trjconv -f md_0_1.xtc -o md_0_1.pdb.Please suggest me the correct script. It depends on what you want. If you want to use the structure from the end of 1 ns, use editconf. Using trjconv to convert an .xtc file to a .pdb file will generate a (potentially) very large .pdb trajectory with all of the frames you saved. Probably not what you want. If there is an intermediate frame you want to utilize, use trjconv -dump. Regarding docking when I did solvent simulation on GUI commercial software, I used to minimize the simulated structure for docking, but i have no clues learnt in gromacs tutorial ( iam new to gromacs) regarding the output whether it is minimized after simulation or not the md.mdp file which i used for the production MD is as below: The structure is minimized after energy minimization, which only provides a reasonable attempt at generating a starting structure. Once the dynamics begin, the goal is to reach a equilibrium sampling of physiologically-relevant configurations. The structure may or may not deviate substantially from the minimized structure (you can gauge that to some extent by RMSD). Probably the purpose of minimization before docking is simply to correct any weird geometry that may be present in the receptor structure -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking
Dear Justin. Thanks for the suggestion, definitely i would run next time for a longer time 2-10 ns. Here, I want to learn the analysis part of the mdrun, In order to locate the lowest energy frame I executed command g_energy -f md_0_1.edr -o PE.xvg and the output was Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-1.2189e+061115.541070.01-1.0927-1092.7 then I had a look at the PE.xvg file, but the values are very close to identify the lowest energy point, i also tried to a have a look at the md_0_1.log file, here also it is tedious and time consuming and the values are close to remember. Can you suggest me how to locate the lowest energy frame, so that i can use the comand (below) to retrieve that particular frame coordinates in PDB file: trjconv -f md_0_1.xtc -o LEconf.pdb -dump framenumber (any frame number- corresponding to the lowest energy) and also please tell the whether the command i am going to use to retrieve the lowest energy configuration is correct. Thanks, Ram On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy configuration of the protein by doing dynamics, i want to collect the structure (coordinates in pdb) representing average of all the frames/configurations produced in MD and also the lowest energy configuration structure (coordinates in PDB) produced during the simulation, which can be used for docking. Please help how to obtain the average structure as well as the lowest energy configuration structure. Average structures are not always meaningful (or even physically-relevant): http://www.gromacs.org/Documentation/Terminology/Average_Structure You can get average structures from, i.e. g_cluster -cl, if you want. As for the lowest energy structure, analyze potential energy, and dump out the frame corresponding to the lowest point. Hopefully you saved coordinates and energies at the same interval :) The potential energy will correspond to that of the system, but hopefully it should give some indication of the lowest energy configuration. I don't know anything about your system, but it will also depend on how much the energy fluctuates as to how relevant this structure might be, and how different it might be from an average. If your structure comes from some model you built, realize that 1 ns is an exceptionally short time frame, especially given the capabilities of modern hardware and the speed of the GROMACS code. You may want to consider running a bit longer to ensure that you really have a stable system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, Thanks. I tried to equilibrate the system in NVT ensemble without constraints, the equilibration completed, but the lipid layers moved apart, so i tried to do simulated annealing procedure mentioned in the trouble shooting section of the tutorial and here also i was able to equilibrate only with the constraints = none option in anneal_npt.mdp file (below). title = Simulated Annealing define = -DPOSRES -DPOSRES_LIPID integrator = md dt = 0.001 nsteps = 50 continuation= no constraints = none constraint-algorithm = lincs lincs-iter = 1 lincs-order = 4 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 Tcoupl = Berendsen tc_grps = Protein DPPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 Pcoupl = Berendsen Pcoupltype = semiisotropic ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = no pbc = xyz DispCorr= EnerPres nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- annealing = single single single annealing_npoints = 2 2 2 annealing_time = 0 500 0 500 0 500 annealing_temp = 0 323 0 323 0 323 Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing as input to npt equilibration. Like I am going to use the following command to run the npt equillibration: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without restraints and increasing the Fmax to 1000, the mdp file used is as follows: Note that I only suggested EM, not necessarily Fmax 1000. You original post contained an even lower Fmax, suggesting that you can do better than 1000. The parameters in my tutorial are somewhat generic; you should alter them to suit your needs. snip Please note that the headers of log files are typically unnecessary when posting the .mdp file. please suggest me is it ok to remove the constraints and run the NVT equillibration. You can try it, but I doubt it will make a difference. Your simulation is crashing before it is even starting, making it very difficult to diagnose. You probably need to re-build the system, using as rigorous criteria as possible during the InflateGRO steps to ensure that you don't have any improper atomic overlap. In my experience, if the simulation is failing at step 0, there is no hope for coaxing the system into working. The configuration simply isn't reasonable. -Justin Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 161.4193.1199 0 0.645591322.796 Heat Capacity Cv: 24.906 J/mol K (factor = 0.332832) Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) -7.96937115.169114.406 0.091665645.8329 i am unable to understand from these parameters, whether the system is ok for future steps. Regarding the gaps in the lipid bilayers,now when i visualized the .trr file in the VMD there were no gaps in the lipid bilayer, that is they did not move apart. Please help. Thanks Ram On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: snip Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing as input to npt equilibration. Like you would anything else. Have the temperature and pressure stabilized? Is your structure reasonable (no gaps, etc)? -Justin Like I am going to use the following command to run the npt equillibration: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without restraints and increasing the Fmax to 1000, the mdp file used is as follows: Note that I only suggested EM, not necessarily Fmax 1000. You original post contained an even lower Fmax, suggesting that you can do better than 1000. The parameters in my tutorial are somewhat generic; you should alter them to suit your needs. snip Please note that the headers of log files are typically unnecessary when posting the .mdp file. please suggest me is it ok to remove the constraints and run the NVT equillibration. You can try it, but I doubt it will make a difference. Your simulation is crashing before it is even starting, making it very difficult to diagnose. You probably need to re-build the system, using as rigorous criteria as possible during the InflateGRO steps to ensure that you don't have any improper atomic overlap. In my experience, if the simulation is failing at step 0, there is no hope for coaxing the system into working. The configuration simply isn't reasonable. -Justin Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, Thanks for the advice and suggestions, will look into the plots and try to run a further NPT equillibration, (here you mean equilibration phase 2 ? without annealing, as in the tutorial).. Please let me know. Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 161.4193.1199 0 0.645591 322.796 Heat Capacity Cv: 24.906 J/mol K (factor = 0.332832) Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) -7.96937115.169114.406 0.0916656 45.8329 i am unable to understand from these parameters, whether the system is ok for future steps. Because simply looking at averages is less useful than looking at the plots. I asked whether the temperature had stabilized, not what it's average value was. Consider this - you're constantly increasing the temperature, so an average is useless. Look at the plot that g_energy gives you and make sure the increase is as you would expect. Probably a further NPT equilibration is needed to make sure that the temperature will remain stable without the influence of annealing. Same thing for pressure - look at the plot. Wide fluctuations will occur, so that's not a problem. The trend is what is important (i.e., running average in xmgrace). Is the pressure leveling off? The average is more meaningful here, and it looks a bit low, but as I advise in my tutorial, equilibrating membrane systems takes a *long* time, anyway. -Justin Regarding the gaps in the lipid bilayers,now when i visualized the .trr file in the VMD there were no gaps in the lipid bilayer, that is they did not move apart. Please help. Thanks Ram On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: snip Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing as input to npt equilibration. Like you would anything else. Have the temperature and pressure stabilized? Is your structure reasonable (no gaps, etc)? -Justin Like I am going to use the following command to run the npt equillibration: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without restraints and increasing the Fmax to 1000, the mdp file used is as follows: Note that I only suggested EM, not necessarily Fmax 1000. You original post contained an even lower Fmax, suggesting that you can do better than 1000. The parameters in my tutorial are somewhat generic; you should alter them to suit your needs. snip Please note that the headers of log files are typically unnecessary when posting the .mdp file. please suggest me is it ok to remove the constraints and run the NVT equillibration. You can try it, but I doubt it will make a difference. Your simulation is crashing before it is even starting, making it very difficult to diagnose. You probably need to re-build the system, using as rigorous criteria as possible during the InflateGRO steps to ensure that you don't have any improper atomic overlap. In my experience, if the simulation is failing at step 0, there is no hope for coaxing the system into working. The configuration simply isn't reasonable. -Justin Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent
Re: [gmx-users] Error during NVT equillibration with nvt.log file
Dear Justin, Thanks, will be back after some trials. Ram On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the advice and suggestions, will look into the plots and try to run a further NPT equillibration, (here you mean equilibration phase 2 ? without annealing, as in the tutorial).. Yes, normal NPT. -Justin Please let me know. Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 161.4193.1199 0 0.645591 322.796 Heat Capacity Cv: 24.906 J/mol K (factor = 0.332832) Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) -7.96937115.169114.406 0.0916656 45.8329 i am unable to understand from these parameters, whether the system is ok for future steps. Because simply looking at averages is less useful than looking at the plots. I asked whether the temperature had stabilized, not what it's average value was. Consider this - you're constantly increasing the temperature, so an average is useless. Look at the plot that g_energy gives you and make sure the increase is as you would expect. Probably a further NPT equilibration is needed to make sure that the temperature will remain stable without the influence of annealing. Same thing for pressure - look at the plot. Wide fluctuations will occur, so that's not a problem. The trend is what is important (i.e., running average in xmgrace). Is the pressure leveling off? The average is more meaningful here, and it looks a bit low, but as I advise in my tutorial, equilibrating membrane systems takes a *long* time, anyway. -Justin Regarding the gaps in the lipid bilayers,now when i visualized the .trr file in the VMD there were no gaps in the lipid bilayer, that is they did not move apart. Please help. Thanks Ram On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: snip Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing as input to npt equilibration. Like you would anything else. Have the temperature and pressure stabilized? Is your structure reasonable (no gaps, etc)? -Justin Like I am going to use the following command to run the npt equillibration: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without restraints and increasing the Fmax to 1000, the mdp file used is as follows: Note that I only suggested EM, not necessarily Fmax 1000. You original post contained an even lower Fmax, suggesting that you can do better than 1000. The parameters in my tutorial are somewhat generic; you should alter them to suit your needs. snip Please note that the headers of log files are typically unnecessary when posting the .mdp file. please suggest me is it ok to remove the constraints and run the NVT equillibration. You can try it, but I doubt it will make a difference. Your simulation is crashing before it is even starting, making it very difficult to diagnose. You probably need to re-build the system, using as rigorous criteria as possible during the InflateGRO steps to ensure that you don't have any improper atomic overlap. In my experience, if the simulation is failing at step 0, there is no hope for coaxing the system into working. The configuration simply isn't reasonable. -Justin Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used
[gmx-users] Error during NVT equillibration
Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded to equillibrate the system using NVT. The mdp file used for NVT equillibration is : title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- and the output error for the mdrun is as under: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002307, max 0.080808 (between atoms 3569 and 3570) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in DPPC in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 31.024508, max 1431.875854 (between atoms 448 and 450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 453455 49.90.1331 0.2004 0.1330 453454 50.50.1231 0.1762 0.1230 451452 89.90.1003
[gmx-users] Error during NVT equillibration with nvt.log file
Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I solvated and ionized sytem and minimized using the following mdp file: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) the output was as follows: Steepest Descents converged to Fmax 500 in 4770 steps Potential Energy = -3.8820288e+05 Maximum force = 4.4803549e+02 on atom 3573 Norm of force = 1.7854408e+01 As the potential energy and Fmax values were agreeable , I proceeded to equillibrate the system using NVT. The mdp file used for NVT equillibration is : title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- and the output error for the mdrun is as under: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002307, max 0.080808 (between atoms 3569 and 3570) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in DPPC in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 31.024508, max 1431.875854 (between atoms 448 and 450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 453455 49.90.1331 0.2004 0.1330 453454 50.50.1231 0.1762 0.1230 451452 89.90.1003 29.4775
Re: [gmx-users] Error during NVT equillibration with nvt.log file
(1997) pp. 1463-1472 --- Thank You --- The number of constraints is 9045 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: Protein_DPPC 1: SOL_CL- PLEASE READ AND CITE THE FOLLOWING REFERENCE G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- There are: 31609 Atoms Max number of connections per atom is 28 Total number of connections is 138849 Max number of graph edges per atom is 4 Total number of graph edges is 48078 Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 4.83e-04 Initial temperature: 333.793 K Started mdrun on node 0 Sun Jul 5 18:04:45 2009 Step Time Lambda 00.00.0 Grid: 10 x 10 x 13 cells Long Range LJ corr.: C6 9.7327e-04 Long Range LJ corr.: Epot -2200.19, Pres: -136.406, Vir:2200.19 Energies (kJ/mol) Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 1.19670e+048.38636e+038.15057e+034.20390e+033.08430e+03 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 4.45274e+035.37063e+043.47509e+06 -2.20019e+03 -4.22052e+05 Coul. recip. Position Rest. PotentialKinetic En. Total Energy -1.63954e+051.03877e+012.98084e+065.03020e+095.03318e+09 Conserved En.Temperature Pressure (bar) Cons. rmsd () 5.03318e+091.91196e+071.03974e+089.31478e+00 and if i remove the the constraints and lowering the time step using the following nvt.mdp file it is running: title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 10; 1 * 10 = 100 ps dt = 0.001 ; 1 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- please suggest me is it ok to remove the constraints and run the NVT equillibration. Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized
[gmx-users] Gromacs installation on the cluster
Dear Gromacs Users, About Gromacs installation on the cluster, we compiled it on both the login node and the computing nodes. I'd like to know which gromacs programs can be run on the login node without disturbing all other users and which ones must be run on the computing nodes (e.g. the MD program). Please give me your suggestions. Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] step 0Segmentation fault
Dear Justin, Thanks for the options suggested. I have used -princ and rotate 0 0 90 options with editconf and was able to place the protein vertically and at the centre of the DPPC bilayer (128 + 3655) from the site provided in the tutorial, but still the part of protein is outside the DPPC layer (examined system.gro (protein newbox +dppc128.gr0) in VMD). The commands used were editconf -f protein_processed.gro -o protein_newbox.gro -c -box 6.41840 6.44350 6.59650 -rotate 0 0 90 cat protein_newbox.gro dppc128.gro system.gro so now, i tried to increase the size of the box by redoing it and using the command editconf -f protein_processed.gro -o protein_newbox.gro -c -box 6.41840 6.44350 6.59650 -d 1.0 -rotate 0 0 90 -bt cubic cat protein_newbox.gro dppc128.gro system1.gro I also used various box types like dodecahedron , octahedron but was unable increase the size of the box and fix the protein in the centre of the dppcbilayer (128 + 3655 H2O). Please suggest me how to correct my command so that all the protein lies in the dppcbilayer and is in the centre and can proceed to inflategro steps, also do i need to use a dppclayer with more lipids like 256 lipid bilayer. Thanks, Ram On Tue, Oct 6, 2009 at 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface of the bilayer, probably this may be the reason for the presence of water molecules to the side of the bilayer when solvated and also lack of minimization during inflategro step. One more thing, I am inserting the protein in Indeed, if your system doesn't actually fit within the unit cell you've defined, you're in for trouble. Always look at your output! lipid bilayer by orienting it using your KALP peptide (.pdb) as reference in VMD and later using editconf to centre the protein using option i.e. -c -box 6.41840 6.44350 6.59650, otherwise if i just use editconf command, it is orienting horizontally instead of vertically, I don't fully understand what you're doing. You also may not be able to use the exact same box that I defined in the tutorial (the original DPPC box). If you've got pieces of your protein protruding out of the unit cell, then you'll need to define a suitably-sized box. Horizontal vs. vertical issues can be solved by editconf -rotate. -Justin i can do the orientation manually using vmd but it is difficult and iam unable to orient it exactly in the centre and vertical in the dppc bilayer. Please suggest some corrections as I am going to reorient and position it in the bilayer and redo the inflategro procedure. Thanks Ram On Tue, Oct 6, 2009 at 4:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp file and the nvt.log files are as follows as in your tutorial: snip Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 9.42e-04 Initial temperature: 503.557 K Started mdrun on node 0 Thu Jun 25 11:30:30 2009 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Large VCM(group Protein_DPPC):-50.08205, 97.99061, 16.32530, Temp-cm: 2.50669e+05 Long Range LJ corr.: C6 2.0307e-03 Long Range LJ corr.: Epot -1862.02, Pres:-184.12, Vir:1862.02 Energies (kJ/mol) Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 1.48814e+048.19090e+038.43857e+036.38969e+03 2.93352e+03 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 4.09831e+035.49186e+047.87055e+09 -1.86202e+03 -1.48414e+05 Coul. recip. Position Rest. PotentialKinetic En. Total Energy -1.53985e+059.50084e+007.87034e+093.08099e+17 3.08099e+17 Conserved En.Temperature Pressure (bar) Cons. rmsd () 3.08099e+172.31982e+151.01551e+167.25066e+04 The information shown here indicates very strongly that you have severe atomic overlap in your starting structure. This is probably from the InflateGRO minimization that did not converge appropriately. Your potential energy is astronomically high, as well as factors like temperature, and thus kinetic energy. The latter are related to trying to constrain an inappropriate starting structure. I would suggest going back to the initial construction stage, figuring out why that minimization didn't converge, and start over from there. Plowing ahead when you get unfavorable results is a recipe for LINCS warnings. -Justin Please diagnose the information and suggest. Thanks ram On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul jalem
Re: [gmx-users] 256 DPPC bilayer
Dear Justin, Thanks. Ram On Mon, Oct 5, 2009 at 7:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am looking for a DPPC bilayer system of 256 and above , can anybody suugest me the site from where I can download Please... Take a pre-equilibrated 128 DPPC bilayer from any number of sites and use genconf or genbox. -Justin Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] step 0Segmentation fault
Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 during the last minimization , later i solvated the protein using a vanderwaal radii for carbon as 0.375, i found some water molecules not in the core of the lipid layer but to the sides, as they were not in the centre i ionated the complex with 13 chloride ions as the charge shown was non-zero total intergral charge 1.3e+01, then i minized the ionized complex with the minim.mdp file in as per justin tutorial, i am following all the mdp files as per the tutorial till now, and was able to obtain Potential Energy = -1.8947278e+05 Maximum force = 9.1642163e+02 on atom 7647 Norm of force = 5.0845932e+01 and then i created the index file ane while running the nvt equilllibrqtion i am getting Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007117, max 0.443345 (between atoms 6311 and 6312) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max 0.068592 (between atoms 6311 and 6312) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 6311 6312 38.80.2064 0.1528 0.1430 starting mdrun 'Protein in DPPC in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 72506.576935, max 3674667.75 (between atoms 707 and 711) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2418 2420 35.30.1338 0.1935 0.1330 2418 2419 37.30.1234 0.1764 0.1230 2414 2416 38.40.1532 0.2058 0.1530 .. .. and finally a step 0Segmentation fault. Can any body suggest me how to rectify the defect and is it the problem with compliation as i am using gromacs 4.0.3 or the memory space or my running the job. Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] step 0Segmentation fault
Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Large VCM(group Protein_DPPC):-50.08205, 97.99061, 16.32530, Temp-cm: 2.50669e+05 Long Range LJ corr.: C6 2.0307e-03 Long Range LJ corr.: Epot -1862.02, Pres:-184.12, Vir:1862.02 Energies (kJ/mol) Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 1.48814e+048.19090e+038.43857e+036.38969e+032.93352e+03 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 4.09831e+035.49186e+047.87055e+09 -1.86202e+03 -1.48414e+05 Coul. recip. Position Rest. PotentialKinetic En. Total Energy -1.53985e+059.50084e+007.87034e+093.08099e+173.08099e+17 Conserved En.Temperature Pressure (bar) Cons. rmsd () 3.08099e+172.31982e+151.01551e+167.25066e+04 Please diagnose the information and suggest. Thanks ram On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 You won't get that magnitude of Epot without water. If you can't reach Fmax 1000, you shouldn't just plow ahead. Analyze where the problem is, because it is unlikely to go away by magic! during the last minimization , later i solvated the protein using a vanderwaal radii for carbon as 0.375, i found some water molecules not in the core of the lipid layer but to the sides, as they were not in the centre i ionated the complex with 13 chloride ions as the charge Did you get rid of these waters? You can always try tweaking the entry in vdwradii.dat for C. As far as those on the sides are concerned, it sounds like the box you've created is too large for the lipids. I wouldn't use this system, because you'll waste a huge amount of time hoping it equilibrates right. shown was non-zero total intergral charge 1.3e+01, then i minized the ionized complex with the minim.mdp file in as per justin tutorial, i am following all the mdp files as per the tutorial till now, and was able to obtain Potential Energy = -1.8947278e+05 Maximum force = 9.1642163e+02 on atom 7647 Norm of force = 5.0845932e+01 That looks fine, but I still think there is an underlying problem in your InflateGRO construction step. and then i created the index file ane while running the nvt equilllibrqtion i am getting Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007117, max 0.443345 (between atoms 6311 and 6312) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length The classic case of blowing up. See either my Advanced Troubleshooting page in the tutorial, or http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you want more specific advice, you'll have to provide information at least about what type of lipid you're using, and what you have in your .mdp file. Can any body suggest me how to rectify the defect and is it the problem with compliation as i am using gromacs 4.0.3 or the memory space or my running the job. Well, first off I'd recommend always using the most current version of the software, not that it's likely to impact your system, but just in general. This is a problem reported to this list almost daily, so please also check the archives. There are literally thousands of posts regarding LINCS warnings and unstable systems. -Justin Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users
Re: [gmx-users] step 0Segmentation fault
Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface of the bilayer, probably this may be the reason for the presence of water molecules to the side of the bilayer when solvated and also lack of minimization during inflategro step. One more thing, I am inserting the protein in lipid bilayer by orienting it using your KALP peptide (.pdb) as reference in VMD and later using editconf to centre the protein using option i.e. -c -box 6.41840 6.44350 6.59650, otherwise if i just use editconf command, it is orienting horizontally instead of vertically, i can do the orientation manually using vmd but it is difficult and iam unable to orient it exactly in the centre and vertical in the dppc bilayer. Please suggest some corrections as I am going to reorient and position it in the bilayer and redo the inflategro procedure. Thanks Ram On Tue, Oct 6, 2009 at 4:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp file and the nvt.log files are as follows as in your tutorial: snip Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 9.42e-04 Initial temperature: 503.557 K Started mdrun on node 0 Thu Jun 25 11:30:30 2009 Step Time Lambda 00.00.0 Grid: 9 x 9 x 9 cells Large VCM(group Protein_DPPC):-50.08205, 97.99061, 16.32530, Temp-cm: 2.50669e+05 Long Range LJ corr.: C6 2.0307e-03 Long Range LJ corr.: Epot -1862.02, Pres:-184.12, Vir:1862.02 Energies (kJ/mol) Angle G96AngleProper Dih. Ryckaert-Bell. Improper Dih. 1.48814e+048.19090e+038.43857e+036.38969e+032.93352e+03 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 4.09831e+035.49186e+047.87055e+09 -1.86202e+03 -1.48414e+05 Coul. recip. Position Rest. PotentialKinetic En. Total Energy -1.53985e+059.50084e+007.87034e+093.08099e+173.08099e+17 Conserved En.Temperature Pressure (bar) Cons. rmsd () 3.08099e+172.31982e+151.01551e+167.25066e+04 The information shown here indicates very strongly that you have severe atomic overlap in your starting structure. This is probably from the InflateGRO minimization that did not converge appropriately. Your potential energy is astronomically high, as well as factors like temperature, and thus kinetic energy. The latter are related to trying to constrain an inappropriate starting structure. I would suggest going back to the initial construction stage, figuring out why that minimization didn't converge, and start over from there. Plowing ahead when you get unfavorable results is a recipe for LINCS warnings. -Justin Please diagnose the information and suggest. Thanks ram On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 You won't get that magnitude of Epot without water. If you can't reach Fmax 1000, you shouldn't just plow ahead. Analyze where the problem is, because it is unlikely to go away by magic! during the last minimization , later i solvated the protein using a vanderwaal radii for carbon as 0.375, i found some water molecules not in the core of the lipid layer but to the sides, as they were not in the centre i ionated the complex with 13 chloride ions as the charge Did you get rid of these waters? You can always try tweaking the entry in vdwradii.dat for C. As far as those on the sides are concerned, it sounds like the box you've created is too large for the lipids. I wouldn't use this system, because you'll waste a huge amount of time hoping it equilibrates right. shown was non-zero total intergral charge 1.3e+01, then i minized the ionized complex with the minim.mdp file in as per justin tutorial, i am following all the mdp files as per the tutorial till now, and was able to obtain Potential Energy = -1.8947278e+05 Maximum force = 9.1642163e+02 on atom 7647 Norm of force = 5.0845932e+01 That looks fine, but I still think there is an underlying problem in your InflateGRO construction step. and then i created the index file ane while running the nvt equilllibrqtion i am getting Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007117, max 0.443345 (between atoms 6311 and 6312
Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water
Dear Justin, Thanks for the suggestions and will be back after sometime after following the trials. Ram On Tue, Sep 29, 2009 at 10:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, I was trying to model a part of the protein involved in the active site and these terminal residues i think have no role in active site as per the literature, so i was removing the residues whose coordinates were not properly assigned (missing H atoms) so the initial terminus changed to serine, we can even find such problems in crystal structures where the coordinates don't get resolved Crystal structures never have H, but we simulate them all the time. Their geometry is largely predictable :) Consider whether or not these deletions will have an effect. While not catalytically active, do they have any role in maintaining the protein's structure? Just my $0.02. Don't chop out what doesn't seem to work; it might (or might not) be important. -Justin properly...I think as the number of residues changed the total charge also changed, these are some of the limitations that i think occur to exactly predict the structure and activity for some proteins. Thanks Ram On Tue, Sep 29, 2009 at 10:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and as per suggestion, now i have corrected the original modelled pdb file and executed the pdb2gmx command with n-terminus option 1 (NH2) and C-terminus option 1 (COOH), now the net charge is 11.00, and the toplogy file has the first and last residues as under: 1 NL 1SER N 1 -0.6614.0067 ; qtot -0.66 2 H 1SER H1 1 0.44 1.008 ; qtot -0.22 3 H 1SER H2 1 0.44 1.008 ; qtot 0.22 4CH1 1SER CA 1 -0.22 13.019 ; qtot 0 5CH2 1SER CB 2 0.266 14.027 ; qtot 0.266 6 OA 1SER OG 2 -0.67415.9994 ; qtot -0.408 7 H 1SER HG 2 0.408 1.008 ; qtot 0 8 C 1SER C 3 0.45 12.011 ; qtot 0.45 9 O 1SER O 3 -0.4515.9994 ; qtot 0 2950 N285PRO N 1280 014.0067 ; qtot 11 2951CH1285PRO CA 1281 0 13.019 ; qtot 11 2952 CH2R285PRO CB 1281 0 14.027 ; qtot 11 2953 CH2R285PRO CG 1282 0 14.027 ; qtot 11 2954 CH2R285PRO CD 1282 0 14.027 ; qtot 11 2955 C285PRO C 1283 0.33 12.011 ; qtot 11.33 2956 O285PRO OT 1283 -0.4515.9994 ; qtot 10.88 2957 OA285PRO O 1283 -0.28815.9994 ; qtot 10.59 2958 H285PRO HO 1283 0.408 1.008 ; qtot 11 Please suggest if it is ok, so that i can continue with the further steps. No, that's your job as a scientist :) Besides, I can't necessarily say. Do those protonation states model reality? Is your model a reasonable representation of a true physical system? Does the net charge make sense? Your original first residue was threonine, now it's serine. What exactly was your fix to this problem? These are the things that you should always consider. Only once you've solved these issues can you proceed with any degree of confidence. -Justin Thanks, Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
[gmx-users] neutralizing membrane protein in lipid bilayer +water
Dear Gromacs users, I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the system and i learnt from Justin tutorial that we can even neutralize it using -conc and -neutral options in conjugation. As I am running a membrane-protein simulation, I would like to know the command which I am using is correct or not. genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 12 -neutral If my command is wrong Please suggest the right one as In future i have to conjugate SOL and CL- ions to create a special index file. Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water
Dear Gromacs Users, Thanks Justin and Marc for the response and you were right. As suggested, i had a view in the modelled protein pdb file and here both the terimus are capped that is as follows; ATOM 1 N THR A 62 -43.095 3.360 19.026 1.00 30.00 N1+ ATOM 4804 OXT PRO A 355 -53.907 34.064 13.899 1.00110.00 O1- then i tried to execute the pdb2gmx command as under, (which i did earlier also): pdb2gmx -f damgomu.pdb -o damgomu_processed.gro -ignh -ter -water spc and selected the Gromos96 53a6 parameter and none options, then the warnings and errors where as follows: Now there are 294 residues with 3043 atoms Making bonds... Warning: Long Bond (12-14 = 0.65447 nm) Warning: Long Bond (1975-1977 = 4.21722 nm) Warning: Long Bond (2050-2052 = 3.24295 nm) Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: atom H is missing in residue THR 1 in the pdb file You might need to add atom H to the hydrogen database of residue THR in the file ff???.hdb (see the manual) Fatal error: There were 1 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing and in the previous run i concatenated -missing option and continued further, then the toplogy was written with the charge of Total charge 12.690 e ,but still the warning persisted of missing H atom in THR1. Please suggest me how to rectify this error and why the total number of atoms in pdb file (4815) are not matching even though the number of residues are matching after pdb2gmx step. Thanks, Ram and selected choose the Gromos96 53a6 parameter and none options On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the system and i learnt from Justin tutorial that we can even neutralize it using -conc and -neutral options in conjugation. As I am running a membrane-protein simulation, I would like to know the command which I am using is correct or not. genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 12 -neutral If my command is wrong Please suggest the right one as In future i have to conjugate SOL and CL- ions to create a special index file. If your protein has a net charge of +12.69, it is probably wrong. Does anything in real life have such a net fractional charge? Go back and evaluate what you have done. Are there missing atoms? Wrong parameters? The genion command you want to use is fine, but is not suitable for your system in its current state. -Justin Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water
Dear Justin, When I observed the toplogy file the first THR moeity was missing in 1 hydrogen atom compared to other Thr in the file so i added one line below the 1st atom nitrogen for hydrogen as under and corrected the qtot to 0, 1 N 1THR N 1 -0.3114.0067 ; qtot -0.31 2 H 1THR H 1 0.31 1.008 ; qtot 0, keeping the rest as the same, and executed the command pdb2gmx and selected the same force field and 1 and 1 for n-terminus and c-terminus, and now there were no errors as under: Now there are 294 residues with 3047 atoms Making bonds... Warning: Long Bond (14-16 = 0.65447 nm) Warning: Long Bond (1977-1979 = 4.21722 nm) Warning: Long Bond (2052-2054 = 3.24295 nm) Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Number of bonds was 3113, now 3108 Generating angles, dihedrals and pairs... Before cleaning: 4938 pairs Before cleaning: 6118 dihedrals There are 1565 dihedrals, 1646 impropers, 4562 angles 4938 pairs, 3108 bonds and 0 virtual sites Total mass 33592.608 a.m.u. Total charge 13.000 e Writing topology but, when i saw the topology file , the same number of atoms are present and no change in the qtot... Why is it that qtot of 13 and the increased number of atoms are not shown in the toplogy file and whether have i selected the wrong options or is it the wrong way of correcting the toplogy file... Thanks, Ram On Tue, Sep 29, 2009 at 8:09 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Thanks Justin and Marc for the response and you were right. As suggested, i had a view in the modelled protein pdb file and here both the terimus are capped that is as follows; ATOM 1 N THR A 62 -43.095 3.360 19.026 1.00 30.00 N1+ ATOM 4804 OXT PRO A 355 -53.907 34.064 13.899 1.00110.00 O1- then i tried to execute the pdb2gmx command as under, (which i did earlier also): pdb2gmx -f damgomu.pdb -o damgomu_processed.gro -ignh -ter -water spc and selected the Gromos96 53a6 parameter and none options, then the warnings and errors where as follows: Why would you choose None? It would seem that you do not, in fact, have capping groups. If atom 1 is the N of THR, then there is no ACE cap before it... Now there are 294 residues with 3043 atoms Making bonds... Warning: Long Bond (12-14 = 0.65447 nm) Warning: Long Bond (1975-1977 = 4.21722 nm) Warning: Long Bond (2050-2052 = 3.24295 nm) These messages generally indicate missing atoms. Investigate what they are and why these errors are coming up. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: atom H is missing in residue THR 1 in the pdb file You might need to add atom H to the hydrogen database of residue THR in the file ff???.hdb (see the manual) This warning comes from the fact that you are telling pdb2gmx to look for capping groups in order to find improper dihedrals, and it appears no such groups exist. Fatal error: There were 1 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing and in the previous run i concatenated -missing option and continued further, then the toplogy was written with the charge of Total charge 12.690 e ,but still the warning persisted of missing H atom in THR1. There is a reason the pdb2gmx help information calls the -missing option dangerous... Please suggest me how to rectify this error and why the total number of atoms in pdb file (4815) are not matching even though the number of residues are matching after pdb2gmx step. Find out which atoms are missing (if any) to fix the long bonds problem, then don't specify None as your termini unless you really have acetyl and amide caps. -Justin Thanks, Ram and selected choose the Gromos96 53a6 parameter and none options On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the system and i learnt from Justin tutorial that we can even neutralize it using -conc and -neutral options in conjugation. As I am running a membrane-protein simulation, I would like to know the command which I am using is correct or not. genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 12 -neutral If my command is wrong Please suggest the right one as In future i have to conjugate SOL and CL- ions to create a special index file. If your protein has a net charge of +12.69, it is probably wrong. Does anything in real life have such a net fractional charge? Go back
Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water
Dear Justin, I was trying to model a part of the protein involved in the active site and these terminal residues i think have no role in active site as per the literature, so i was removing the residues whose coordinates were not properly assigned (missing H atoms) so the initial terminus changed to serine, we can even find such problems in crystal structures where the coordinates don't get resolved properly...I think as the number of residues changed the total charge also changed, these are some of the limitations that i think occur to exactly predict the structure and activity for some proteins. Thanks Ram On Tue, Sep 29, 2009 at 10:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and as per suggestion, now i have corrected the original modelled pdb file and executed the pdb2gmx command with n-terminus option 1 (NH2) and C-terminus option 1 (COOH), now the net charge is 11.00, and the toplogy file has the first and last residues as under: 1 NL 1SER N 1 -0.6614.0067 ; qtot -0.66 2 H 1SER H1 1 0.44 1.008 ; qtot -0.22 3 H 1SER H2 1 0.44 1.008 ; qtot 0.22 4CH1 1SER CA 1 -0.22 13.019 ; qtot 0 5CH2 1SER CB 2 0.266 14.027 ; qtot 0.266 6 OA 1SER OG 2 -0.67415.9994 ; qtot -0.408 7 H 1SER HG 2 0.408 1.008 ; qtot 0 8 C 1SER C 3 0.45 12.011 ; qtot 0.45 9 O 1SER O 3 -0.4515.9994 ; qtot 0 2950 N285PRO N 1280 014.0067 ; qtot 11 2951CH1285PRO CA 1281 0 13.019 ; qtot 11 2952 CH2R285PRO CB 1281 0 14.027 ; qtot 11 2953 CH2R285PRO CG 1282 0 14.027 ; qtot 11 2954 CH2R285PRO CD 1282 0 14.027 ; qtot 11 2955 C285PRO C 1283 0.33 12.011 ; qtot 11.33 2956 O285PRO OT 1283 -0.4515.9994 ; qtot 10.88 2957 OA285PRO O 1283 -0.28815.9994 ; qtot 10.59 2958 H285PRO HO 1283 0.408 1.008 ; qtot 11 Please suggest if it is ok, so that i can continue with the further steps. No, that's your job as a scientist :) Besides, I can't necessarily say. Do those protonation states model reality? Is your model a reasonable representation of a true physical system? Does the net charge make sense? Your original first residue was threonine, now it's serine. What exactly was your fix to this problem? These are the things that you should always consider. Only once you've solved these issues can you proceed with any degree of confidence. -Justin Thanks, Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nvt.gro
Dear Justin, When I used the energy mininized system for NPT annealing with position restraints on lipids and there was no separation. So, I think I can proceed now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the Molecular Dynamics for data collection(1ns).What do you suggest, is it the right way i am following..as i will be not be using NVT equillibration anywhere through out the process. Thanks, Ram On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested, i increased the force constant in the Z dimension from 1000 to 1, and did the NVT equillibration, but still the gap existed, then i gave the output of nvt equillibration that is nvt.gro as input for the NPT anneling simulation (suggested as with position constraints, 1000) and simulated and here also i had gap .between layers when npt.gro was viewed in VMD. I have a query that is can I use nvt equllibrated system as input for NPT simualated annealing or should I use the initial ionized and minimized system for the NPT annaelated simulation, as the gap is still persisting... Use the energy-minimized system as the input into annealing. I have no idea why this separation would be happening in this system, unless the box has been prepared improperly. I chose the KALP-DPPC system because it is very robust in everything we've tried to subject it to. -Justin Thanks Ram On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested in the tutorial by you i applied the lipid position restraints, while running the NVT equillibration, but after the job is finished, when i observed the nvt.gro file in VMD, still there is a gap between the lipid bilayers but this time the gap is not so large as it was in the earlier run (as discussed earlier in previous email). As I was already running the NPT equillibration(which I obtained after the earlier NVT job, which ended in large gap between layers), i just wanted to observe it and here there is no gap in between the layers i.e. in npt.gro. Please suggest me what to do to lower the gap after NVT equillibration even after applying the lipid restraints and is it ok for my NPT equillibration as there are no gaps between the layers after this NPT equillibration. The gap arises because the lipids (when free to move) are attracted to the water above and below the bilayer. If the protein is restrained, it doesn't move. The box size in NVT is fixed, so the system is trying to fill it. It could be that your box was inappropriately assigned (too large), but maybe not. I am surprised that, even when using position restraints, the lipids still separated at all. Did you use the lipid_posre.itp file that I provide on the tutorial site? It has always worked well for me in such cases. You could also try increasing the force constant in the z-dimension. The other option is to do NPT simulated annealing, as I also suggest in the troubleshooting page. Using NPT allows the box to deform in response to the system, so you will probably get less weird behavior. I have found that both NVT with PR and simulated annealing can get the job done. -Justin Thanks Ram On Tue, Sep 22, 2009 at 8:25 PM, ram bio rmbio...@gmail.com mailto:rmbio...@gmail.com mailto:rmbio...@gmail.com mailto:rmbio...@gmail.com wrote: Dear Justin, Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section. Ram On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact in between the bilayers, but the the two layers got separated or else it is like the peptide bridging the the two halves of the lipid bilayer with gap in between the layers and also found few water molecules to the sides of the peptide or in the gap mentioned betwwn the layers. Please let me know is the simulation going on normally
Re: [gmx-users] nvt.gro
Dear Justin, Thanks for the options and suggestions, will be back after some trials with modelled proteins. Ram On Mon, Sep 28, 2009 at 6:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, When I used the energy mininized system for NPT annealing with position restraints on lipids and there was no separation. So, I think I can proceed now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the Molecular Dynamics for data collection(1ns).What do you suggest, is it the right way i am following..as i will be not be using NVT equillibration anywhere through out the process. I think that should be fine. There is really no prescribed way to do equilibration, necessarily. Everyone has their own method. If you can stabilize the temperature and pressure prior to data collection, then you've done enough, in general. Just be aware that my definition of data collection simply means that you're remove restraints from anything that was previously restrained. Collecting data for membrane protein systems often occurs after 10-20 ns (or more), to allow for re-orientation of lipids, which is very slow. -Justin Thanks, Ram On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested, i increased the force constant in the Z dimension from 1000 to 1, and did the NVT equillibration, but still the gap existed, then i gave the output of nvt equillibration that is nvt.gro as input for the NPT anneling simulation (suggested as with position constraints, 1000) and simulated and here also i had gap .between layers when npt.gro was viewed in VMD. I have a query that is can I use nvt equllibrated system as input for NPT simualated annealing or should I use the initial ionized and minimized system for the NPT annaelated simulation, as the gap is still persisting... Use the energy-minimized system as the input into annealing. I have no idea why this separation would be happening in this system, unless the box has been prepared improperly. I chose the KALP-DPPC system because it is very robust in everything we've tried to subject it to. -Justin Thanks Ram On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested in the tutorial by you i applied the lipid position restraints, while running the NVT equillibration, but after the job is finished, when i observed the nvt.gro file in VMD, still there is a gap between the lipid bilayers but this time the gap is not so large as it was in the earlier run (as discussed earlier in previous email). As I was already running the NPT equillibration(which I obtained after the earlier NVT job, which ended in large gap between layers), i just wanted to observe it and here there is no gap in between the layers i.e. in npt.gro. Please suggest me what to do to lower the gap after NVT equillibration even after applying the lipid restraints and is it ok for my NPT equillibration as there are no gaps between the layers after this NPT equillibration. The gap arises because the lipids (when free to move) are attracted to the water above and below the bilayer. If the protein is restrained, it doesn't move. The box size in NVT is fixed, so the system is trying to fill it. It could be that your box was inappropriately assigned (too large), but maybe not. I am surprised that, even when using position restraints, the lipids still separated at all. Did you use the lipid_posre.itp file that I provide on the tutorial site? It has always worked well for me in such cases. You could also try increasing the force constant in the z-dimension. The other option is to do NPT simulated annealing, as I also suggest in the troubleshooting page. Using NPT allows the box to deform in response to the system, so you will probably get less weird behavior. I have found that both NVT with PR and simulated annealing can get the job done. -Justin Thanks Ram On Tue, Sep 22, 2009 at 8:25 PM, ram bio rmbio...@gmail.com mailto:rmbio...@gmail.com mailto:rmbio...@gmail.com mailto:rmbio
Re: [gmx-users] nvt.gro
Dear Justin, As suggested in the tutorial by you i applied the lipid position restraints, while running the NVT equillibration, but after the job is finished, when i observed the nvt.gro file in VMD, still there is a gap between the lipid bilayers but this time the gap is not so large as it was in the earlier run (as discussed earlier in previous email). As I was already running the NPT equillibration(which I obtained after the earlier NVT job, which ended in large gap between layers), i just wanted to observe it and here there is no gap in between the layers i.e. in npt.gro. Please suggest me what to do to lower the gap after NVT equillibration even after applying the lipid restraints and is it ok for my NPT equillibration as there are no gaps between the layers after this NPT equillibration. Thanks Ram On Tue, Sep 22, 2009 at 8:25 PM, ram bio rmbio...@gmail.com wrote: Dear Justin, Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section. Ram On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact in between the bilayers, but the the two layers got separated or else it is like the peptide bridging the the two halves of the lipid bilayer with gap in between the layers and also found few water molecules to the sides of the peptide or in the gap mentioned betwwn the layers. Please let me know is the simulation going on normally or there is an defect or wrong going on, as the nvt equillibration was proper as i think i continued for the next equillibration that is npt for 1ns. You shouldn't continue blindly if you get weird results. Please see the Advanced Troubleshooting page (part of the tutorial!), because I specifically address the issue of a bilayer separating: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html -Justin Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] nvt.gro
Dear Gromacs Users, I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact in between the bilayers, but the the two layers got separated or else it is like the peptide bridging the the two halves of the lipid bilayer with gap in between the layers and also found few water molecules to the sides of the peptide or in the gap mentioned betwwn the layers. Please let me know is the simulation going on normally or there is an defect or wrong going on, as the nvt equillibration was proper as i think i continued for the next equillibration that is npt for 1ns. Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nvt.gro
Dear Justin, Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section. Ram On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact in between the bilayers, but the the two layers got separated or else it is like the peptide bridging the the two halves of the lipid bilayer with gap in between the layers and also found few water molecules to the sides of the peptide or in the gap mentioned betwwn the layers. Please let me know is the simulation going on normally or there is an defect or wrong going on, as the nvt equillibration was proper as i think i continued for the next equillibration that is npt for 1ns. You shouldn't continue blindly if you get weird results. Please see the Advanced Troubleshooting page (part of the tutorial!), because I specifically address the issue of a bilayer separating: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html -Justin Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Inflategro
Dear Gromacs Users, While I was runing the Justin's tutorial that is KALP-15 in DPPC , I have some queries regarding the INFLATEGRO, Please have patience to read and answer my queries: 1) does the system.gro should include the position restrained file of KALP_newbox.gro after running genrestr, as i combined the ouput of genestr to dppc128.gro to generate system.gro. 2) should both the box vectors in system.gro to be deleted or just the ones under KALP structure, the other being at the end of the file. 3)then I updated the system.gro file to 17503 atoms from 138 atoms and executed this command: perl INFLATEGRO system.gro 4 DPP 14 inflated_system.gro 5 areaperlipid.dat the output was as under: Reading. Scaling lipids There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 2 lipids within cut-off range... 1 will be removed from the upper leaflet... 1 will be removed from the lower leaflet... Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 2640 Protein Y-min/max: 2539 X-range: 14 AY-range: 14 A Building 14 X 14 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 2 nm^2 Area per lipid: 10.4716089904762 nm^2 Area per protein, upper half: 1.75 nm^2 Area per lipid, upper leaflet : 10.475577244 nm^2 Area per protein, lower half: 2 nm^2 Area per lipid, lower leaflet : 10.4716089904762 nm^2 Writing Area per lipid... Done! then, i updated the topol_dppc_top to 126 lipids ; System specifications [ system ] 126-Lipid DPPC Bilayer [ molecules ] ; molecule name nr. DPPC 126 SOL 3655 and also updated the number of atoms in system.gro to 17403 and added 126 DPPC and 3655 SOL to topol.top file and executed the grompp command for minimization as under: grompp -f minim.mdp -c system.gro -p topol.top -o em.tpr minim.mdp parameters are as under: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform define = -DSTRONG_POSRES ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) the ouput of grompp was : Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 813 of the 2346 non-bonded parameter combinations ERROR 1 [file topol.top, line 535]: No default G96Angle types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 904]: System has non-zero total charge: 4.11e+00 processing coordinates... WARNING 1 [file topol.top, line 904]: Bad box in file system.gro Generated a cubic box6.612 x6.639 x6.741 Warning: atom name 6439 in topol.top and system.gro does not match (OW - C1) Warning: atom name 6440 in topol.top and system.gro does not match (HW1 - C2) Warning: atom name 6441 in topol.top and system.gro does not match (HW2 - C3) Warning: atom name 6442 in topol.top and system.gro does not match (OW - N4) Warning: atom name 6443 in topol.top and system.gro does not match (HW1 - C5) Warning: atom name 6444 in topol.top and system.gro does not match (HW2 - C6) Warning: atom name 6445 in topol.top and system.gro does not match (OW - O7) Warning: atom name 6446 in topol.top and system.gro does not match (HW1 - P8) Warning: atom name 6447 in topol.top and system.gro does not match (HW2 - O9) Warning: atom name 6448 in topol.top and system.gro does not match (OW - O10) Warning: atom name 6449 in topol.top and system.gro does not match (HW1 - O11) Warning: atom name 6450 in topol.top and system.gro does not match
