[gmx-users] regarding table for water water interactions
Hai all, My system is just a water Spc model. I am trying to create a table.xvg which would deal with nonbonded intearction for water-water for say SPC model. If i have to calculate the potential i have to consider the interaction between 1.O of water1--O of water 2(LJ+COLOUMB) [CREATED A TABLE that containsr, f (r), -f (r), g(r),-g (r), h(r) and -h (r) ] 2.H of water 1--O of water 2(COLOUMB)[ are tables needed ?] 3.H of water 1--H of water 2(COLOUMB) [are tables needed ?] for 2 and 3rd case should i create 2 tables respectively ? if not how is the potential is calculated for the the last two cases ?and if it has to be to created since the lennard jones part say g(r),-g (r), h(r) and -h (r) is zero for all values of r should i just create a table with r,f(r)and -f'(r) for last two cases? looking forward for reply. regards, sree. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to make a membrane system with 512 DPPCs
Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where? If you have a 128-lipid membrane: genconf -f 128.gro -o 512.gro -nbox 2 2 1 -Justin We also tried to build a 512 lipids system manually. First by means of VMD where we combined 4 128 pre-assembled membranes together thus creating one single file with 512 lipids, however during energy minimization the whole membrane shattered and scattered bits of lipid outside the defined box dimensions. Another problem was that after ionization 2 of the membranes parts (128+128 lipids) were merged and 1 got deleted. The second method was by running a self-assembly simulation (270 ns) on gromacs using the Martini forcefield, yet we did not get a single membrane but double bi-layers with water in between. Any suggestion is appreciated. Albert and Jiang.-- 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. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to make a membrane system with 512 DPPCs
On 2011-05-25 07:58:18AM -0500, Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where? We also tried to build a 512 lipids system manually. First by means of VMD where we combined 4 128 pre-assembled membranes together thus creating one single file with 512 lipids, however during energy minimization the whole membrane shattered and scattered bits of lipid outside the defined box dimensions. Another problem was that after ionization 2 of the membranes parts (128+128 lipids) were merged and 1 got deleted. The second method was by running a self-assembly simulation (270 ns) on gromacs using the Martini forcefield, yet we did not get a single membrane but double bi-layers with water in between. Any suggestion is appreciated. I don't do anything with DPPC (yet), but another thing that might be doable is take the POPC template from VMD's membrane plugin and substitute the oleoyl chain with a copy of the palmitoyl chain, then use the membrane plugin to create the bilayer (it takes Angstrom dimensions for the bilayer size), strip the waters, parameterize the single dppc to an itp, genbox the # of waters you care for, then equilibrate... -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to make a membrane system with 512 DPPCs
On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote: Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where? If you have a 128-lipid membrane: genconf -f 128.gro -o 512.gro -nbox 2 2 1 Wasn't there a warning about PBC and compact structures when using the PDBs from Peter Tieleman? Aren't we supposed to unwrap those structures with trjconv before actually using them in any sort of meaningful way? See also http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html on generating a dummy tpr for feeding into trjconv. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to make a membrane system with 512 DPPCs
Peter C. Lai wrote: On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote: Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where? If you have a 128-lipid membrane: genconf -f 128.gro -o 512.gro -nbox 2 2 1 Wasn't there a warning about PBC and compact structures when using the PDBs from Peter Tieleman? Aren't we supposed to unwrap those structures with trjconv before actually using them in any sort of meaningful way? See also http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html on generating a dummy tpr for feeding into trjconv. Sure, you need an intact starting structure before doing anything like this. There are other sources of membranes, not just Tieleman's site, many of which have already been corrected for PBC effects. The OP did not state the source of the 128-lipid membranes in question, so I did not presuppose any particular starting configuration. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charmm36 in Gromacs: missing dihedrals
Dear Mark and Justin, Thanks for the quick reply. I must have misunderstood the procedure. I was assuming that the generated top file should include the actual values used for the Urea-Bradley terms. Previously I have only included molecules using an itp file and was expecting similar behaviour. For anyone interested. I got the system to work by removing the waters from the input file and running pdb2gmx. Then using editconf on the pdb with waters. Then I manually edited the top file to add the correct number of water molecules into the [ molecules ] directive. Then I needed to rename the water molecules correctly to correspond to the correct names in the tips3p.itp file in the charmm36 directory. Following this I ran grompp successfully. Many thanks, Jon On 25 May 2011 14:20, Justin A. Lemkul jalem...@vt.edu wrote: Jon Fuller wrote: Dear all, I thought that I would reply to this thread as I am having similar problems and there didn't seem to be an obvious solution. I wanted to run a simulation of a POPE bilayer using the Charmm36 parameters from the Gromacs website. So I used pdb2gmx to generate a .top file. I used the input file from this website: wget http://terpconnect.umd.edu/~jbklauda/research/download/pope80-c36npt.pdb pdb2gmx -f pope80-c36npt.pdb -o pope.pdb -p pope.top -ff charmm36 (I then selected option 3 (tips3p charmm water)) I found that whilst pdb2gmx completes 'successfully', no bond, angle or dihedral terms are generated in the resulting top file. I found this behaviour when running both pdb2gmx version 4.5.3 and version 4.5.4. As a further check I also found the same behaviour if I used the charmm27 parameters. I found this related thread, but there was no obvious solution to the problem. I see no problem here. You have all the necessary directives ([bonds], [angles], and [dihedrals]) in the .top you show. The actual parameters for those bonded terms are not written to the .top; they are taken from ffbonded.itp when running grompp. Now, if grompp complains about something being missing, that's a separate issue. -Justin As far as I can tell I am using a reasonable procedure. Can anyone spot something that I'm doing wrong to cause this behaviour? I have pasted the output from pdb2gmx below and truncated results from the top file below this. Many thanks in advance, Jon :-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 4.5.3 (-: ... ... Using the Charmm36 force field in directory charmm36.ff Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIPS3P CHARMM TIP 3-point with LJ on H's (note: twice as slow in GROMACS) 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None 3 Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.r2b Reading pope80-c36npt.pdb... Read 17683 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 256 residues with 17683 atoms chain #res #atoms 1 ' ' 2641 17683 All occupancies are one Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36) Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.rtp Residue 41 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/dna.rtp Residue 53 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/lipids.rtp Residue 89 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/rna.rtp Residue 101 Sorting it all out... Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.hdb Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/lipids.hdb Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.n.tdb Opening force field file /home/fullerjn/Software/gromacs-4.5.3_install/share/gromacs/top/charmm36.ff/aminoacids.c.tdb Processing chain 1 (17683 atoms, 2641 residues) There are 80 donors and 0 acceptors There are 0 hydrogen bonds Warning: Starting residue POPE1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPE2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue POPE3 in chain not identified as Protein/RNA/DNA. Warning: Starting
Re: [gmx-users] dipole moment
I want to see the change in dipole moment alond the simulation. NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] dipole moment
Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] dipole moment
On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless (position dependent). Otherwise the charges are constant and the fluctuation in bond length (if you have a flexible molecule) will be small, or zero with constraints. You should think what you want to get out. What experiment you want to compare to. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] sphere around a protein
Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following commands: editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro genbox -cp his1.gro -cs li_sol.gro * 1li.gro is:* 1 Li ion 1 1LI+ LI1 1.736 0.839 0.257 1.86824 1.86824 1.86824 *onlyli.gro is:* 1 Li ion 1 1LI+ LI1 7.500 7.500 7.500 15.0 15.0 15.0 *mix.gro ( pre-made mix of 1:1 :: water: methanol)* li_sol.gro des look like a sphere after seeingin vmd. his1.gro is: UNNAMED 14 1HISH N1 0.000 0.000 0.000 1HISHH12 -0.033 0.000 -0.094 1HISHH23 -0.033 -0.082 0.047 1HISHCA4 0.146 0.000 0.000 1HISHCB5 0.204 0.120 -0.077 1HISHCG6 0.291 0.076 -0.190 1HISH ND17 0.240 0.009 -0.299 1HISH HD18 0.145 -0.014 -0.315 1HISH CD29 0.425 0.089 -0.215 1HISH CE1 10 0.345 -0.019 -0.382 1HISH NE2 11 0.458 0.027 -0.333 1HISH HE2 12 0.549 0.020 -0.374 1HISH C 13 0.195 0.000 0.146 1HISH O 14 0.118 0.000 0.242 2.50220 0.24060 2.47531 I get the following error yet again: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. -- Thanks a lot in advance. Sorry about reviving few days old thread. Thanks, SN On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul jalem...@vt.edu wrote: shivangi nangia wrote: Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Please provide the exact command that gives the error. I cannot reproduce this using a shell value less than half a box vector. You may also want to try starting from a clean directory - get rid of old files and intermediates so you're sure you're using the right files. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] sphere around a protein
shivangi nangia wrote: Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following commands: editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro genbox -cp his1.gro -cs li_sol.gro * 1li.gro is:* 1 Li ion 1 1LI+ LI1 1.736 0.839 0.257 1.86824 1.86824 1.86824 *onlyli.gro is:* 1 Li ion 1 1LI+ LI1 7.500 7.500 7.500 15.0 15.0 15.0 *mix.gro ( pre-made mix of 1:1 :: water: methanol)* li_sol.gro des look like a sphere after seeingin vmd. his1.gro is: UNNAMED 14 1HISH N1 0.000 0.000 0.000 1HISHH12 -0.033 0.000 -0.094 1HISHH23 -0.033 -0.082 0.047 1HISHCA4 0.146 0.000 0.000 1HISHCB5 0.204 0.120 -0.077 1HISHCG6 0.291 0.076 -0.190 1HISH ND17 0.240 0.009 -0.299 1HISH HD18 0.145 -0.014 -0.315 1HISH CD29 0.425 0.089 -0.215 1HISH CE1 10 0.345 -0.019 -0.382 1HISH NE2 11 0.458 0.027 -0.333 1HISH HE2 12 0.549 0.020 -0.374 1HISH C 13 0.195 0.000 0.146 1HISH O 14 0.118 0.000 0.242 2.50220 0.24060 2.47531 I get the following error yet again: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Look at the box vectors of his1.gro - a sphere of solvent with a radius of 6 cannot fit inside a box that is 2.5 x 0.2 x 2.5 nm^3. -Justin -- Thanks a lot in advance. Sorry about reviving few days old thread. Thanks, SN On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shivangi nangia wrote: Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Please provide the exact command that gives the error. I cannot reproduce this using a shell value less than half a box vector. You may also want to try starting from a clean directory - get rid of old files and intermediates so you're sure you're using the right files. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-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 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] dipole moment
Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along the simulation. Can I calculate the velocity autocorrelation function for a bond. Nilesh On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote: On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless (position dependent). Otherwise the charges are constant and the fluctuation in bond length (if you have a flexible molecule) will be small, or zero with constraints. You should think what you want to get out. What experiment you want to compare to. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] query regarding replica exchange
Hi, I am planning to run replica exchange simulation using gromacs 4.0.7 . I have read the manual about REMD. Only thing I wanted to know is that how I can specify the name of host-machines where I am planning to run the simulations. I have 10 different quad-core computers each intra-connected with the other each running OPENMPI. I want to run 20 replica each using 2 cores in parallel. So, I was wondering whether I have to create any file containing the names of those machines . If so, can someone give an example of format of the file which contain those names ? Finally, what keyword I should use in mdrun to specify that file for running replica exchange. Also, I am not using any PBS for submitting jobs. Sanku-- 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] dipole moment
On 2011-05-25 20.42, Nilesh Dhumal wrote: Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along the simulation. Can I calculate the velocity autocorrelation function for a bond. Of course. How about g_velacc Nilesh On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote: On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless (position dependent). Otherwise the charges are constant and the fluctuation in bond length (if you have a flexible molecule) will be small, or zero with constraints. You should think what you want to get out. What experiment you want to compare to. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular oxygen and hydrogen in same group (manually). Nilesh On Wed, May 25, 2011 11:59 am, David van der Spoel wrote: On 2011-05-25 17.36, Nilesh Dhumal wrote: I want to see the change in dipole moment alond the simulation. g_dipoles -h NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles with a suitable index file would do it. The sum of charges has to be zero of course. I am using gromacs version 4.0.7. Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of CellMolec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] sphere around a protein
Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? Thanks a lot, SN On Wed, May 25, 2011 at 1:18 PM, Justin A. Lemkul jalem...@vt.edu wrote: shivangi nangia wrote: Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following commands: editconf -f 1li.gro -c -box 15 15 15 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro genbox -cp his1.gro -cs li_sol.gro * 1li.gro is:* 1 Li ion 1 1LI+ LI1 1.736 0.839 0.257 1.86824 1.86824 1.86824 *onlyli.gro is:* 1 Li ion 1 1LI+ LI1 7.500 7.500 7.500 15.0 15.0 15.0 *mix.gro ( pre-made mix of 1:1 :: water: methanol)* li_sol.gro des look like a sphere after seeingin vmd. his1.gro is: UNNAMED 14 1HISH N1 0.000 0.000 0.000 1HISHH12 -0.033 0.000 -0.094 1HISHH23 -0.033 -0.082 0.047 1HISHCA4 0.146 0.000 0.000 1HISHCB5 0.204 0.120 -0.077 1HISHCG6 0.291 0.076 -0.190 1HISH ND17 0.240 0.009 -0.299 1HISH HD18 0.145 -0.014 -0.315 1HISH CD29 0.425 0.089 -0.215 1HISH CE1 10 0.345 -0.019 -0.382 1HISH NE2 11 0.458 0.027 -0.333 1HISH HE2 12 0.549 0.020 -0.374 1HISH C 13 0.195 0.000 0.146 1HISH O 14 0.118 0.000 0.242 2.50220 0.24060 2.47531 I get the following error yet again: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Look at the box vectors of his1.gro - a sphere of solvent with a radius of 6 cannot fit inside a box that is 2.5 x 0.2 x 2.5 nm^3. -Justin -- Thanks a lot in advance. Sorry about reviving few days old thread. Thanks, SN On Mon, May 9, 2011 at 6:21 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shivangi nangia wrote: Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Please provide the exact command that gives the error. I cannot reproduce this using a shell value less than half a box vector. You may also want to try starting from a clean directory - get rid of old files and intermediates so you're sure you're using the right files. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-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
Re: [gmx-users] sphere around a protein
shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? That's what genion is for. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] sphere around a protein
Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? That's what genion is for. I take that back, genion doesn't work for polyatomic ions. The better approach is to construct your system with solute, ions (which in this case are just other molecules floating around), etc, before adding the sphere of solvent. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] sphere around a protein
Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all the ions that I had added in the box? Some might still be in open space of the box? Thanks, SN On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? That's what genion is for. I take that back, genion doesn't work for polyatomic ions. The better approach is to construct your system with solute, ions (which in this case are just other molecules floating around), etc, before adding the sphere of solvent. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] sphere around a protein
shivangi nangia wrote: Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all the ions that I had added in the box? Some might still be in open space of the box? You need to start with whatever molecules you want to solvate in a suitable configuration. Insert them with genbox -ci -nmol and a small box, then solvate with the sphere as before. -Justin Thanks, SN On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro -shell 3 -o li_sol.gro genbox -cp li_sol.gro -cs mix.gro -shell 3 -o 6nmshell.gro editconf -f his20.gro -d 0 -o onlyhis.gro editconf -f onlyhis.gro -c -box 12 12 12 -o hisinbox.gro genbox -cp hisinbox.gro -cs 6nmshell.gro -o 6sys.gro Now I need to add few more Li ions and anions in the sphere. I tried doing that, genbox -cp 6sys.gro -ci 1dhb.gro -nmol 20 -o added_dhb.gro -p topol.top (1dhb.gro is 2,5-dihydrobenzoic acid anion) But, since the sphere 6sys.gro is essentially in a box, the dhb anions ...some got randomly placed inside the sphere and some in the open spaces of the box in which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? That's what genion is for. I take that back, genion doesn't work for polyatomic ions. The better approach is to construct your system with solute, ions (which in this case are just other molecules floating around), etc, before adding the sphere of solvent. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-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 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] query regarding replica exchange
You will need a file formatted like the following: node0 slots=4 max_slots=4 node1 slots=4 max_slots=4 ... node9 slots=4 max_slots=4 You will then need to use the -hostfile option to supply the filename to either mpiexec or mpirun (not mdrun). -- Josh On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote: Hi, I am planning to run replica exchange simulation using gromacs 4.0.7 . I have read the manual about REMD. Only thing I wanted to know is that how I can specify the name of host-machines where I am planning to run the simulations. I have 10 different quad-core computers each intra-connected with the other each running OPENMPI. I want to run 20 replica each using 2 cores in parallel. So, I was wondering whether I have to create any file containing the names of those machines . If so, can someone give an example of format of the file which contain those names ? Finally, what keyword I should use in mdrun to specify that file for running replica exchange. Also, I am not using any PBS for submitting jobs. Sanku -- 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 -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- 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] query regarding replica exchange
I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated . From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, May 25, 2011 7:16:44 PM Subject: Re: [gmx-users] query regarding replica exchange On 26/05/2011 8:50 AM, Joshua L. Phillips wrote: You will need a file formatted like the following: node0 slots=4 max_slots=4 node1 slots=4 max_slots=4 ... node9 slots=4 max_slots=4 You will then need to use the -hostfile option to supply the filename to either mpiexec or mpirun (not mdrun). Indeed. Details will vary with the nature of the MPI installation - but it's an MPI issue, not a GROMACS issue. The only relevant detail is that you wish every pair of cores assigned to a replica to be on the same machine. The above approach will generally achieve that. Mark -- Josh On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote: Hi, I am planning to run replica exchange simulation using gromacs 4.0.7 . I have read the manual about REMD. Only thing I wanted to know is that how I can specify the name of host-machines where I am planning to run the simulations. I have 10 different quad-core computers each intra-connected with the other each running OPENMPI. I want to run 20 replica each using 2 cores in parallel. So, I was wondering whether I have to create any file containing the names of those machines . If so, can someone give an example of format of the file which contain those names ? Finally, what keyword I should use in mdrun to specify that file for running replica exchange. Also, I am not using any PBS for submitting jobs. Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query regarding replica exchange
Sanku M wrote: I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated . This is a question for your sysadmin. Most such implementations ignore hostfiles for this very reason. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_velacc
Hello, I am trying to calculate the velocity autocorrelation function of OH bond in glucose molecule. The calculate velocity autocorrelation function is not smooth. Its fluctuating a lot so I am geting wide/think line. Why I am not geting a smooth line? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with replica exchange
Hi, I am having a problem in running replica exchange simulation over multiple nodes. To run the simulation for 16 replicas over two 8-core processors, I generated a hostfile as follows: yethiraj30 slots=8 max_slots=8 yethiraj31 slots=8 max_slots=8 These two machines are intra-connected and I have installed openmpi Then If I try to run the replica exchange simulation using the following command:mpirun -np 16 --hostfile hostfile mdrun_4mpi -s topol_.tpr -multi 16 -replex 100 log_replica_test But I find following error and mdrun does not proceed at all : NNODES=16, MYRANK=0, HOSTNAME=yethiraj30NNODES=16, MYRANK=1, HOSTNAME=yethiraj30NNODES=16, MYRANK=4, HOSTNAME=yethiraj30NNODES=16, MYRANK=2, HOSTNAME=yethiraj30NNODES=16, MYRANK=6, HOSTNAME=yethiraj30NNODES=16, MYRANK=3, HOSTNAME=yethiraj30NNODES=16, MYRANK=5, HOSTNAME=yethiraj30NNODES=16, MYRANK=7, HOSTNAME=yethiraj30[yethiraj30][[22604,1],0][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],4][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],6][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],1][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],3][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)[yethiraj30][[22604,1],2][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113)NNODES=16, MYRANK=10, HOSTNAME=yethiraj31NNODES=16, MYRANK=12, HOSTNAME=yethiraj31 I am not sure how to resolve this issue. In general, I can go from one machine to another without any problem using ssh. But, when I am trying to run openmpi over both the machines, I get this error. Any help will be appreciated. Jagannath -- 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] g_energy unable to -skip
Hello When I try to specify -skip with g_energy it still outputs the data from all frames into the .xvg file. I have to use eneconv -dt to strip out the data from said .edr (which yields a lot of data not found error messages) in order to get a compacted .xvg dataset... -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with replica exchange
On 26/05/2011 12:25 PM, jagannath mondal wrote: Hi, I am having a problem in running replica exchange simulation over multiple nodes. To run the simulation for 16 replicas over two 8-core processors, I generated a hostfile as follows: yethiraj30 slots=8 max_slots=8 yethiraj31 slots=8 max_slots=8 These two machines are intra-connected and I have installed openmpi Then If I try to run the replica exchange simulation using the following command: mpirun -np 16 --hostfile hostfile mdrun_4mpi -s topol_.tpr -multi 16 -replex 100 log_replica_test But I find following error and mdrun does not proceed at all : NNODES=16, MYRANK=0, HOSTNAME=yethiraj30 NNODES=16, MYRANK=1, HOSTNAME=yethiraj30 NNODES=16, MYRANK=4, HOSTNAME=yethiraj30 NNODES=16, MYRANK=2, HOSTNAME=yethiraj30 NNODES=16, MYRANK=6, HOSTNAME=yethiraj30 NNODES=16, MYRANK=3, HOSTNAME=yethiraj30 NNODES=16, MYRANK=5, HOSTNAME=yethiraj30 NNODES=16, MYRANK=7, HOSTNAME=yethiraj30 [yethiraj30][[22604,1],0][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113) [yethiraj30][[22604,1],4][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113) [yethiraj30][[22604,1],6][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113) [yethiraj30][[22604,1],1][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113) [yethiraj30][[22604,1],3][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113) [yethiraj30][[22604,1],2][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.0.31 failed: No route to host (113) NNODES=16, MYRANK=10, HOSTNAME=yethiraj31 NNODES=16, MYRANK=12, HOSTNAME=yethiraj31 I am not sure how to resolve this issue. In general, I can go from one machine to another without any problem using ssh. But, when I am trying to run openmpi over both the machines, I get this error. Any help will be appreciated. Sorry, this is a problem of MPI configuration, not GROMACS, if six of your processors are not talking properly. You'll need to read the documentation and/or talk with your sysadmins. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query regarding replica exchange
Often, a PBS submission system will provide the host information to MPI automatically. However, you will have to refer to the documentation for your particular cluster (or talk to the sysadmin, as Justin mentioned) to determine if your particular cluster behaves this way, which MPI process startup program you need to use (mpiexec, mpirun, ibrun, etc.) and any additional flags needed to run parallel jobs on that cluster. -- Josh On Wed, 2011-05-25 at 22:03 -0400, Justin A. Lemkul wrote: Sanku M wrote: I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated . This is a question for your sysadmin. Most such implementations ignore hostfiles for this very reason. -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 -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to calculate lateral pressure for monolayer compression or expansion
Dear Users, As I want to simulate surfactant monolayer with different molecular area in order to reproduce the LB experiment (isotherm plot). So I have to fix a number of surfactant molecules but only surface area is changed by applying the lateral pressure. However, I don't know how to calculate the lateral pressure for the monolayer compression or expansion. Could anyone please suggest me how to do this? Thank you Dr. Sriprajak Krongsuk Physics Department, Faculty of Science Khon Kaen University, Thailand Tel. (Mobile) 081-2630095 -- 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] (no subject)
Dear Sir/Madam, In gromacs tutor we have water .gro file for spc potential. How to get .gro files from spc216.pdb of different potentials like tip3p tip4p ... etc. -- With Regards, Ravi Kumar Venkatraman, c/o Prof. Siva Umapathy, IPC Dept., IISc., Bangalore, INDIA. Phone No: +91-9686933963 -- 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] (no subject)
On 26/05/2011 2:55 PM, Ravi Kumar Venkatraman wrote: Dear Sir/Madam, In gromacs tutor we have water .gro file for spc potential. How to get .gro files from spc216.pdb of different potentials like tip3p tip4p ... etc. You don't need a file in .gro format, and coordinate files for any of the three-point water models are interchangeable. There are other files in $GMXLIB/share/top for the other water models. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
