[gmx-users] g_rms (rmsd vs residue no)
Hi g_rms gives us a xvg file containing rmsd vs time. I want obtain rmsd vs residue number. what option should be used with g_rms? Any help will highly appreciated! -- 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] g_rms (rmsd vs residue no)
Hi Leila, There is no such option. This has been discussed on the list quite recently. You can try to be creative with index groups to get what you want. Cheers, Tsjerk On Wed, Dec 9, 2009 at 9:56 AM, leila karami karami.lei...@gmail.com wrote: Hi g_rms gives us a xvg file containing rmsd vs time. I want obtain rmsd vs residue number. what option should be used with g_rms? Any help will highly appreciated! -- 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] g_rms (rmsd vs residue no)
Hi Leila, Try the -od option in g_rmsf. Regards, João On Wed, Dec 9, 2009 at 8:56 AM, leila karami karami.lei...@gmail.comwrote: Hi g_rms gives us a xvg file containing rmsd vs time. I want obtain rmsd vs residue number. what option should be used with g_rms? Any help will highly appreciated! -- 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] g_confrms
Hi I used command : [g_confrms -f1 initial.gro -f2 final.gro -n1 1.ndx -n2 2.ndx -o fit.pdb] to obtain superimposed structure of initial and final structures. I saw fit.pdb file by vmd but fit.pdb obtained was very mixed,busy and unclear. is my manner true? is there other method for this purpose? Any help will highly appreciated! -- 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] gromacs..
Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks Henry From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 8, 2009 12:49:18 PM Subject: Re: [gmx-users] gromacs.. Henry Ynag wrote: Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
Fw: [gmx-users] gromacs..
Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks Henry From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 8, 2009 12:49:18 PM Subject: Re: [gmx-users] gromacs.. Henry Ynag wrote: Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] include file mechanism pope.itp in protein-membrane system
Hi!! I am using the include file mechanism to define the topology of my protein-membrane system. I have a problem regarding the pope.itp file. I use a modified version of the pope.itp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies (see below).That is accordingly with the pdb file that I am using ( see bellow). However when using grompp I got this warning: Warning: atom name 7542 in papc_topol2.top and system-clean-120xy.pdb does not match (H1 - N) Warning: atom name 7543 in papc_topol2.top and system-clean-120xy.pdb does not match (O1 - H1) Warning: atom name 7544 in papc_topol2.top and system-clean-120xy.pdb does not match (CA - H2) as if none of the atoms that belong to pope in the pdb match the respective itp file. Maybe I am wrong but seems to me that the the atoms are actually matching.. any suggestions are welcome... Irene system.top--- #include ffoplsaa.itp #include protein-only.itp #include pope.itp #include popg.itp #include tip3p.itp #include ions.itp ---pope.itp--- [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 LNL 1POPE N 0-0.5000 14.0067; qtot:0.7 2 H1POPE H1 0 0.4000 1.0080; qtot:0.36 3 H1POPE H2 0 0.4000 1.0080; qtot:0.72 4 H1POPE H3 0 0.4000 1.0008; qtot:1.08 5 LH2 1POPE CA 0 0.3000 14.0270; qtot:1.0 6 LC2 1POPE CB 1 0.4000 14.0270; qtot:1.0 7 LP1POPE P 1 1.70030.9738; qtot:2.3 8 LOM 1POPE OB 1-0.80015.9994; qtot:1.5 9 LOM 1POPE OC 1-0.80015.9994; qtot:0.7 10 LOS 1POPE OD 1-0.70015.9994; qtot:0 11 LOS 1POPE OA 1-0.80015.9994; qtot:0.54 12 LC2 1POPE CC 2 0.40014.0270; qtot:0.08 13 LH1 1POPE CD 2 0.30013.0190; qtot:0.52 14 LOS 1POPE OG 2-0.70015.9994; qtot:-0.14 15 LC 1POPEC2A 2 0.7000 12.0110; qtot:0.56 16 LO 1POPE OH 2-0.70015.9994; qtot:0.0 17 LP2 1POPEC2B 3 0.0 14.0270; qtot: 18 LC2 1POPE CE 4 0.5014.0270; qtot: 19 LOS 1POPE OE 4 -0.7015.9994; qtot: 20 LC 1POPEC1A 4 0.8012.0110; qtot: 21 LO 1POPE OF 4 -0.6015.9994; qtot: 22 LP2 1POPEC1B 5 014.0270; qtot: 23 LP2 1POPEC2C 6 014.0270; qtot: 24 LP2 1POPEC2D 7 014.0270; qtot: 25 LP2 1POPEC2E 8 014.0270; qtot: 26 LP2 1POPEC2F 9 014.0270; qtot: 27 LP2 1POPEC2G 10 014.0270; qtot: 28 LP2 1POPEC2H 11 014.0270; qtot: 29 LH1 1POPEC2I 12 013.0190; qtot: 30 LH1 1POPEC2J 13 013.0190; qtot: 31 LP2 1POPEC2K 14 014.0270; qtot: 32 LP2 1POPEC2L 15 014.0270; qtot: 33 LP2 1POPEC2M 16 014.0270; qtot: 34 LP2 1POPEC2N 17 014.0270; qtot: 35 LP2 1POPEC2O 18 014.0270; qtot: 36 LP2 1POPEC2P 19 014.0270; qtot: 37 LP2 1POPEC2Q 20 014.0270 ; tail2 38 LP3 1POPEC2R 21 015.0350 ; tail2 39 LP2 1POPEC1C 22 014.0270; qtot: 40 LP2 1POPEC1D 23 014.0270; qtot: 41 LP2 1POPEC1E 24 014.0270; qtot: 42 LP2 1POPEC1F 25 014.0270; qtot: 43 LP2 1POPEC1G 26 014.0270; qtot: 44 LP2 1POPEC1H 27 014.0270; qtot: 45 LP2 1POPEC1I 28 014.0270; qtot: 46 LP2 1POPEC1J 29 014.0270; qtot: 47 LP2 1POPEC1K 30 014.0270; qtot: 48 LP2 1POPEC1L 31 014.0270; qtot: 49 LP2 1POPEC1M 32
[gmx-users] How to calculate the PMF?
Dear all, It is the first time that I use gromacs 4.04 to calculate PMF. I have some question needed to be clarified. 1. ; ; pull code for PMF pull= Unbrella;unbrella,constraint pull_geometry = Distance;distance ,direction,cylinder,position pull_dim = N N Y pull_group0 = DPPC pull_group1 = DEN pull_nstxout= 100 pull_nstfout = 100 pull_init1 = 3.8 pull_k1 = 1000 Is there any relationship between the steps for pull_nstxout and pull_nsfout. Must they be the same( e.g. 100, 100)? How to choose them? 2. It seems that there are only two output file: pullx.xvg and pullf.xvg. Is it right? are there other files for the input of g_wham? 3. What other thing I must take care of for calculation of PMF Thanks in advance. -- wende -- 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] gromacs..
Henry Yang wrote: Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks No. As I said in my previous message, you will have to come up with some script (or use some other software) to multiply those box vectors and divide by the # of lipids per leaflet. You can then plot those derived data. -Justin Henry *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 8, 2009 12:49:18 PM *Subject:* Re: [gmx-users] gromacs.. Henry Ynag wrote: Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -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 mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] include file mechanism pope.itp in protein-membrane system
irene farabella wrote: Hi!! I am using the include file mechanism to define the topology of my protein-membrane system. I have a problem regarding the pope.itp file. I use a modified version of the pope.itp from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies (see below).That is accordingly with the pdb file that I am using ( see bellow). However when using grompp I got this warning: Warning: atom name 7542 in papc_topol2.top and system-clean-120xy.pdb does not match (H1 - N) Warning: atom name 7543 in papc_topol2.top and system-clean-120xy.pdb does not match (O1 - H1) Warning: atom name 7544 in papc_topol2.top and system-clean-120xy.pdb does not match (CA - H2) as if none of the atoms that belong to pope in the pdb match the respective itp file. Maybe I am wrong but seems to me that the the atoms are actually matching.. any suggestions are welcome... Well, if you've modified the pope.itp file, then that could be a source of error, but without substantially more information about what you've done, there's nothing to comment on there. The other potential problem is that the content of the [molecules] directive must be the same as the order of the species in the coordinate file. You may be seeing mismatches because things are out of place in the topology. -Justin Irene system.top--- #include ffoplsaa.itp #include protein-only.itp #include pope.itp #include popg.itp #include tip3p.itp #include ions.itp ---pope.itp--- [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 LNL 1POPE N 0-0.5000 14.0067 ; qtot:0.7 2 H1POPE H1 0 0.4000 1.0080; qtot:0.36 3 H1POPE H2 0 0.4000 1.0080; qtot:0.72 4 H1POPE H3 0 0.4000 1.0008; qtot:1.08 5 LH2 1POPE CA 0 0.3000 14.0270 ; qtot:1.0 6 LC2 1POPE CB 1 0.4000 14.0270 ; qtot:1.0 7 LP1POPE P 1 1.70030.9738 ; qtot:2.3 8 LOM 1POPE OB 1-0.80015.9994 ; qtot:1.5 9 LOM 1POPE OC 1-0.80015.9994 ; qtot:0.7 10 LOS 1POPE OD 1-0.70015.9994 ; qtot:0 11 LOS 1POPE OA 1-0.80015.9994 ; qtot:0.54 12 LC2 1POPE CC 2 0.40014.0270 ; qtot:0.08 13 LH1 1POPE CD 2 0.30013.0190 ; qtot:0.52 14 LOS 1POPE OG 2-0.70015.9994 ; qtot:-0.14 15 LC 1POPEC2A 2 0.7000 12.0110 ; qtot:0.56 16 LO 1POPE OH 2-0.70015.9994 ; qtot:0.0 17 LP2 1POPEC2B 3 0.0 14.0270 ; qtot: 18 LC2 1POPE CE 4 0.5014.0270 ; qtot: 19 LOS 1POPE OE 4 -0.7015.9994 ; qtot: 20 LC 1POPEC1A 4 0.8012.0110 ; qtot: 21 LO 1POPE OF 4 -0.6015.9994 ; qtot: 22 LP2 1POPEC1B 5 014.0270; qtot: 23 LP2 1POPEC2C 6 014.0270; qtot: 24 LP2 1POPEC2D 7 014.0270; qtot: 25 LP2 1POPEC2E 8 014.0270; qtot: 26 LP2 1POPEC2F 9 014.0270; qtot: 27 LP2 1POPEC2G 10 014.0270; qtot: 28 LP2 1POPEC2H 11 014.0270; qtot: 29 LH1 1POPEC2I 12 013.0190; qtot: 30 LH1 1POPEC2J 13 013.0190; qtot: 31 LP2 1POPEC2K 14 014.0270; qtot: 32 LP2 1POPEC2L 15 014.0270; qtot: 33 LP2 1POPEC2M 16 014.0270; qtot: 34 LP2 1POPEC2N 17 014.0270; qtot: 35 LP2 1POPEC2O 18 014.0270; qtot: 36 LP2 1POPEC2P 19 014.0270; qtot: 37 LP2 1POPEC2Q 20 014.0270 ; tail2 38 LP3 1POPEC2R 21 015.0350 ; tail2 39 LP2 1POPEC1C 22 014.0270; qtot: 40 LP2 1POPEC1D 23 014.0270; qtot: 41 LP2 1POPEC1E 24 014.0270; qtot: 42 LP2 1POPEC1F 25 014.0270;
Re: [gmx-users] gromacs..
On Dec 9, 2009, at 3:41 PM, Justin A. Lemkul wrote: Henry Yang wrote: Hi there, Thanks for telling how to calculate the area per lipid. But at the same time if I want to draw a plot of area per lipid vs time then how can I proceed? Any gromacs tool comes out which I can use? thanks You can obviously plot the box dimensions as function of time as suggested by Justin and then multiply the X and Y component (if the membrane is in the xy plan) and divide by the number of lipid per leaflet ... No. As I said in my previous message, you will have to come up with some script (or use some other software) to multiply those box vectors and divide by the # of lipids per leaflet. You can then plot those derived data. -Justin Henry *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 8, 2009 12:49:18 PM *Subject:* Re: [gmx-users] gromacs.. Henry Ynag wrote: Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -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 mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb vs xtc with g_bond and g_angle
Hi I am trying to extract bond lengths and bond angles from a trajectory file using g_bond and g_angle. Original simulation generated a xtc file which I then converted to pdb using trjconv. Turns out that for some frames bond lengths (and angles) computed using the xtc file are different from that computed using pdb! And the pdb values are correct as they match with measurements in VMD. Sample outputs for the two cases are below. Any idea what is causing this discrepancy ? I am using GMX 4.0.5. Regards Sandeep *SAMPLE OUTPUT (distance.xvg) * * * matching values are in bold. -PDB $ g_bond_d -f propane4.pdb -n bond.ndx -s md.tpr @ xaxis label Time (ps) @ yaxis label Distance (nm) *0. 0.15820* 1. 0.14859 2. 0.17248 3. 0.15750 4. 0.15835 *5. 0.15367 6. 0.15394 7. 0.15878* 8. 0.15211 9. 0.15482 10. 0.14874 -XTC $ g_bond_d -f propane4.xtc -n bond.ndx -s md.tpr @ xaxis label Time (ps) @ yaxis label Distance (nm) *0. 0.15820* 1. 0.05791 2. 0.13811 3. 0.14364 4. 0.13509 *5. 0.15367 6. 0.15394 7. 0.15878* 8. 0.06900 9. 0.07710 10. 0.08916 -- 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] New to Gromacs -- looking for insights
Dear all, I am researching optimization for MPI parallel programs. As I saw Gromacs seems to use MPI and my idea is to test some of the program transformations I am aware of to improve the performance. The main problem is how should I get started with Gromacs? :) Which of the provided programs rely on MPI calls? and furthermore, where can I find some significant input files? Thanks in advance for the help. regards, S. Pellegrini -- 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] pdb vs xtc with g_bond and g_angle
sandeep somani wrote: Hi I am trying to extract bond lengths and bond angles from a trajectory file using g_bond and g_angle. Original simulation generated a xtc file which I then converted to pdb using trjconv. Turns out that for some frames bond lengths (and angles) computed using the xtc file are different from that computed using pdb! And the pdb values are correct as they match with measurements in VMD. Sample outputs for the two cases are below. Any idea what is causing this discrepancy ? I am using GMX 4.0.5. Sounds like a periodicity artefact from your use of trjconv to me. Mark *SAMPLE OUTPUT (distance.xvg) * * * matching values are in bold. -PDB $ g_bond_d -f propane4.pdb -n bond.ndx -s md.tpr @ xaxis label Time (ps) @ yaxis label Distance (nm) *0. 0.15820* 1. 0.14859 2. 0.17248 3. 0.15750 4. 0.15835 *5. 0.15367 6. 0.15394 7. 0.15878* 8. 0.15211 9. 0.15482 10. 0.14874 -XTC $ g_bond_d -f propane4.xtc -n bond.ndx -s md.tpr @ xaxis label Time (ps) @ yaxis label Distance (nm) *0. 0.15820* 1. 0.05791 2. 0.13811 3. 0.14364 4. 0.13509 *5. 0.15367 6. 0.15394 7. 0.15878* 8. 0.06900 9. 0.07710 10. 0.08916 -- 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] New to Gromacs -- looking for insights
Simone Pellegrini wrote: Dear all, I am researching optimization for MPI parallel programs. As I saw Gromacs seems to use MPI and my idea is to test some of the program transformations I am aware of to improve the performance. The main problem is how should I get started with Gromacs? :) Which of the provided programs rely on MPI calls? and furthermore, where can I find some significant input files? The first ports of call are the manual and the numerous tutorials posted online: http://www.gromacs.org/Documentation/Tutorials The only MPI-enabled program is mdrun. -Justin Thanks in advance for the help. regards, S. Pellegrini -- 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] path
Hello, I have installed the Groamcs 4.0.5 version on linux machime. During the simulation I found that prog. take the /usr/share/gromacs/top (here gromacs 3.3 version) instead of /usr/local/gromacs/share/gromacs/top (here is Groamcs 4.0.5 version. Can you tell How to modify path sothat I can use groamcs 4.0.5 version. 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/search before posting! Please don't post (un)subscribe requests 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] New to Gromacs -- looking for insights
Simone Pellegrini wrote: Dear all, I am researching optimization for MPI parallel programs. As I saw Gromacs seems to use MPI and my idea is to test some of the program transformations I am aware of to improve the performance. It's already fairly good - be sure to read the GROMACS 4 paper. Up to about 64 processors on good network hardware, GROMACS runs are usually quite CPU-bound, so it is not a good candidate for improvement through any MPI optimization. The MPMD communication pattern with PME at high parallelism is interesting, though, and might benefit from task layout that is cunning with respect to the network topology. The main problem is how should I get started with Gromacs? :) Which of the provided programs rely on MPI calls? and furthermore, where can I find some significant input files? Only mdrun uses MPI. Look on the web or the GROMACS wiki for some pointers to tutorials to learn how to construct a workflow that will lead to a meaningful test. 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] amber ports folder in GROMACS
Dear GROMACS users, I m trying to port amber force fields to my GROMACS in my local folder on cluster. as is written here http://chemistry.csulb.edu/ffamber/ (5)Files for each force field are located in a seperate subdirectory, such as ffamber94/ for the Cornell potential. Copy the desired ffamber* files to the top directory in your gromacs distribution. but does that relates only to amber force field as far is in my top directory there are no subdirectories for GROMOS etc force fields? Sincerely yours, Andrey -- 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] amber ports folder in GROMACS
Andrew Voronkov wrote: Dear GROMACS users, I m trying to port amber force fields to my GROMACS in my local folder on cluster. as is written here http://chemistry.csulb.edu/ffamber/ (5) Files for each force field are located in a seperate subdirectory, such as ffamber94/ for the Cornell potential. Copy the desired ffamber* files to the top directory in your gromacs distribution. but does that relates only to amber force field as far is in my top directory there are no subdirectories for GROMOS etc force fields? Correct. The ffamber ports are simply organized as subdirectories for convenience. -Justin Sincerely yours, Andrey -- 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] combining minimization and md
I was wondering, is there a way you can prepare the parameter files so it will do a minimization followed by molecular dynamics? I think its a feature some other Molecular Dynamics apps support but I have not seen any example mdp files that describe this. -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] combining minimization and md
Jack Shultz wrote: I was wondering, is there a way you can prepare the parameter files so it will do a minimization followed by molecular dynamics? I think its a feature some other Molecular Dynamics apps support but I have not seen any example mdp files that describe this. No. It is listed under the development to-do's, but no such features are currently supported. It should be rather easily to script such a procedure, though. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Asking for help into crystalline organic Compound Simulations
Reinaldo Molina Ruiz wrote: Dear Professor David Spoel My name is Reinaldo Molina, I am trying to start in the Molecular-Dynamic Simulation of Crystalline Organic Compounds, but I have affronted serial difficulties with Gromacs Parameters for find out the suitable condition to run a simulations. Please, could you provide me some advises or a place where I can find a tutorial in order to perform starting from X ray’s structure? Please put further questions on the mailing list. I suspect your box is too large, since 288 atoms should fit in 1.5 nm^3 or something. You have to use the exact unitcell (may be triclinic). I will appreciate any advice from you, and I want to know if OPLS is a suitable forcefield to simulate crystalline compounds. My main aim is to simulate the vapor pressure of crystalline organic compounds a different temperature. I built the topology of my compounds and applied the space-group symmetry operations to my unit cell. I have a big box with 16 molecules and I got my .gro file: Pure UC-244 288 1MNVFC11 0.784 1.182 2.759 1MNVFC22 0.762 1.056 2.826 1MNVFC33 0.868 1.041 2.936 1MNVFC44 0.952 1.159 2.935 . . . 16MNVF H17 287 2.930 2.652 1.042 16MNVF H18 288 2.856 2.547 0.920 6.0 6.0 6.0 my top file ; Include forcefield parameters #include ffoplsaa.itp ; Include UC-244 pure #include uc244.itp [ system ] Pure UC-244 [ molecules ] ;molecule namenumber MNVF 16 And my itp file, together with em.mdp and md.mdp In this file I used PME as coulomtype, pressure coupling Parribekki-Rahman and also SHAKE calculations, but I become a error always at 60 ps that said: Program mdrun_mpi, VERSION 4.0.5 Source code file: ../../../../src/mdlib/ns.c, line: 2295 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. In waiting for you time and kindness, Sincerely yours, Reinaldo Molina Universidad Central Marta Abreu de Las Villas. http://www.uclv.edu.cu - Universidad 2010, La Habana, del 8 al 12 de febrero de 2010. http://www.universidad2010.cu -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RDF plot. This is weird!
Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1h 45 min to be complete. The plot does not follow the normal trend I see for rdf plot ie first peak higher than the second, so I know something is wrong but I don't know what. Can someone take a look at my graph and tell me what is wrong with my system or with my computation? Thank you, Lum RDF_SOLSOL 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to add NaCl to bulk liquid water
Hi, All Given the configuration file of a bulk SPCE water system, how can I add a Na+ and Cl- into it using some gromacs or vmd tool? I tried autoionize tool in vmd, but failed due to no psf file; then I tried autopsfgen tool, failed again due to no proper topology file that can recognize SPCE water. Thanks in advance ! Guozhen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to add NaCl to bulk liquid water
GZ Zhang wrote: Hi, All Given the configuration file of a bulk SPCE water system, how can I add a Na+ and Cl- into it using some gromacs or vmd tool? I tried autoionize tool in vmd, but failed due to no psf file; then I tried autopsfgen tool, failed again due to no proper topology file that can recognize SPCE water. Thanks in advance ! Please see the man page for genion. -Justin Guozhen -- 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] Reproducing Chain Tilt on DPPC gel phase with Martini FF
Dear all, I would like to simulate a DPPC membrane in gel phase using Martini Force Field. As stated on Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model, CPL 135 (2005) 223-244 the correct 30º angle chain tilt for DPPC might be reproduced by reducing the acyl chain spheres volume by 10%. So far, I have tried changing sigma and epsilon for C1-C1 pair interaction without success. Best regards Cesar Avila -- 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] Fwd: RDF plot. This is weird!
Hi, I am forwarding the message and the attachment because I did not see my message in the inbox of gmx-users; I saw only the attached file. Please, can the text be included? Thank you. -- Forwarded message -- From: Lum Nforbi lumngwe...@gmail.com Date: Wed, Dec 9, 2009 at 11:59 AM Subject: RDF plot. This is weird! To: gmx-users@gromacs.org Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1h 45 min to be complete. The plot does not follow the normal trend I see for rdf plot ie first peak higher than the second, so I know something is wrong but I don't know what. Can someone take a look at my graph and tell me what is wrong with my system or with my computation? Thank you, Lum RDF_SOLSOL 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/search before posting! Please don't post (un)subscribe requests 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] Fwd: RDF plot. This is weird!
It came through just fine for me; see my reply that I posted earlier: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047358.html -Justin Lum Nforbi wrote: Hi, I am forwarding the message and the attachment because I did not see my message in the inbox of gmx-users; I saw only the attached file. Please, can the text be included? Thank you. -- Forwarded message -- From: *Lum Nforbi* lumngwe...@gmail.com mailto:lumngwe...@gmail.com Date: Wed, Dec 9, 2009 at 11:59 AM Subject: RDF plot. This is weird! To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1h 45 min to be complete. The plot does not follow the normal trend I see for rdf plot ie first peak higher than the second, so I know something is wrong but I don't know what. Can someone take a look at my graph and tell me what is wrong with my system or with my computation? Thank you, Lum -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: RDF plot. This is weird!
Hi Justin, I chose my whole system of 2000 water molecules. I discussed this plot with someone and they said that rdf can be plotted for atoms as well as whole molecules and that the shape of my rdf plot was not a problem of my having used the whole system (I am not really sure about this). The length of my run was 8 ns (8000 ps). The energy values don't change much so I think the system is pretty equilibrated. I have included below the results of my last two run continuations of 2000 ps each (I had to extend the run to ensure equlibration): For the extension from 4000 ps to 6000 ps, I have the results, Statistics over 301 steps [ 0. thru 6000.0005 ps ], 10 data sets All averages are exact over 301 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -79499.3288.958 288.95 -0.00126651 -7.59903 Kinetic En. 14960.4 192.23192.206 -0.00176262 -10.5757 Total Energy -64538.9357.576357.538 -0.00302911 -18.1747 Temperature 299.9613.854273.85379 -3.5341e-05 -0.212046 Pressure (bar) 0.925645194.462194.455 0.000953178 5.71907 Box-X 3.94525 0.00514608 0.00514608 0 0 Box-Y 3.94525 0.00514608 0.00514608 0 0 Box-Z 3.94525 0.00514608 0.00514608 0 0 Volume 61.4083 0.240493 0.240493 -3.12077e-07 -0.00187246 Density (SI)974.322 3.80683.80679 4.31424e-06 0.0258854 Heat Capacity Cv: 12.4749 J/mol K (factor = 0.000165103) Isothermal Compressibility: 2.2742e-05 /bar Adiabatic bulk modulus:43971.6 bar For extension from 6000 ps to 8000 ps, the results are: Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.000164281 1.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thanks, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: RDF plot. This is weird!
Lum Nforbi wrote: Hi Justin, I chose my whole system of 2000 water molecules. I discussed this plot with someone and they said that rdf can be plotted for atoms as well as whole molecules and that the shape of my rdf plot was not a problem of my having used the whole system (I am not really sure about this). I would disagree. The default method of RDF calculation is by atom (see g_rdf -h, specifically the -rdf flag!), as RDF are often plotted between pairs of atom types (O-O, O-H, H-H in the case of water). Try again using a proper calculation method. -Justin The length of my run was 8 ns (8000 ps). The energy values don't change much so I think the system is pretty equilibrated. I have included below the results of my last two run continuations of 2000 ps each (I had to extend the run to ensure equlibration): For the extension from 4000 ps to 6000 ps, I have the results, Statistics over 301 steps [ 0. thru 6000.0005 ps ], 10 data sets All averages are exact over 301 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -79499.3288.958 288.95 -0.00126651 -7.59903 Kinetic En. 14960.4 192.23192.206 -0.00176262 -10.5757 Total Energy -64538.9357.576357.538 -0.00302911 -18.1747 Temperature 299.9613.854273.85379 -3.5341e-05 -0.212046 Pressure (bar) 0.925645194.462194.455 0.000953178 5.71907 Box-X 3.94525 0.00514608 0.00514608 0 0 Box-Y 3.94525 0.00514608 0.00514608 0 0 Box-Z 3.94525 0.00514608 0.00514608 0 0 Volume 61.4083 0.240493 0.240493 -3.12077e-07 -0.00187246 Density (SI)974.322 3.80683.80679 4.31424e-06 0.0258854 Heat Capacity Cv: 12.4749 J/mol K (factor = 0.000165103) Isothermal Compressibility: 2.2742e-05 /bar Adiabatic bulk modulus:43971.6 bar For extension from 6000 ps to 8000 ps, the results are: Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.000164281 1.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thanks, Lum -- 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] Problems with calculating Cv and Cp
Dear all, I have run an 8 ns NPT simulation of 2000 molecules of TIP3P water and I have a very low Cv value of 12.4748 J/mol K (factor = 0.000164481). The result is below. I ignored this value and have tried using formulas for Cv that I found in the two books: Allen and Tildesley J. M. Haile but I can't come out with the right answer. Has anyone ever calculated Cv or Cp for water manually from scratch and gotten the right answer? If so, please, could you give me the details of what you did? Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift -- - Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.000164281 1.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thank you, Lum -- 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] Problems with calculating Cv and Cp
Lum, You'll have better luck if you perform a few simulations at different temperatures at the same pressure and mole number, and then numerically differentiate the resulting enthalpy. I believe that the default heat capacity that Gromacs will print out is only valid for NVE simulations, and I am not sure of the formulas that you are referring to from Allen and Tildesley J.M. Haile. Also, don't expect your calculated heat capacity with TIP3P to agree the experimental value. You should under-predict the experimental value. Lastly, depending on what you are interested in, you may have better luck with a water model other than TIP3P. Hope this helps, Andrew ___ ___ Andrew Paluch Department of Chemical and Biomolecular Engineering University of Notre Dame du Lac apal...@nd.edu ___ ___ On Dec 9, 2009, at 8:18 PM, Lum Nforbi wrote: Dear all, I have run an 8 ns NPT simulation of 2000 molecules of TIP3P water and I have a very low Cv value of 12.4748 J/mol K (factor = 0.000164481). The result is below. I ignored this value and have tried using formulas for Cv that I found in the two books: Allen and Tildesley J. M. Haile but I can't come out with the right answer. Has anyone ever calculated Cv or Cp for water manually from scratch and gotten the right answer? If so, please, could you give me the details of what you did? Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift -- - Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.0001642811.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thank you, Lum -- 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] fftw vs cmkl
Just wondering if anyone has done a comparison of GROMACS complied using fftw versus cmkl? SC tech suggested that cmkl might be a bit faster, but can't find any mention of someone making a comparison between them anywhere, searching users list and web for cmkl (is there may be another term used for it?). Are running a test myself to see, so will report back with that once it is done. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat-- 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] fftw vs cmkl
Dallas B. Warren wrote: Just wondering if anyone has done a comparison of GROMACS complied using fftw versus cmkl? SC tech suggested that cmkl might be a bit faster, but can't find any mention of someone making a comparison between them anywhere, searching users list and web for cmkl (is there may be another term used for it?). Are running a test myself to see, so will report back with that once it is done. On vayu http://nf.nci.org.au/facilities/vayu/hardware.php I found FFTW 3.2.2 and Intel MKL to be equivalent in GROMACS compiled with icc. 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] Charge neutralization
Hey all, I am trying to examine couplings between Mg+2 ions and a peptide with a -5 charge. I would like to optimize couplings and have considered using a +1 charge from the system. I read that GROMACS can do this and that in theory it should have the same effect as adding ions but it is not standard practice. For future simulations I plan to increase the [Mg+2] and am worried about couplings from Cl- if I were to use Cl- to neutralize the excess positive charge. Is it ok to use the system to neutralize these charges? Or is that considered a bad experimental design? Thanks for you feedback! Arden Perkins -- 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] Charge neutralization
Arden Perkins wrote: Hey all, I am trying to examine couplings between Mg+2 ions and a peptide with a -5 charge. I would like to optimize couplings and have considered using a +1 charge from the system. I read that GROMACS can do this and that in theory it should have the same effect as adding ions but it is not standard practice. For future simulations I plan to increase the [Mg+2] and am worried about couplings from Cl- if I were to use Cl- to neutralize the excess positive charge. Is it ok to use the system to neutralize these charges? Or is that considered a bad experimental design? What do you mean by using the system to neutralize these charges? 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] energy minimization
I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ;Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no - I am getting the ouput as following- Steepest Descents converged to machine precision in 67 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.0967048e+06 Maximum force = 3.7720719e+04 on atom 5530 Norm of force = 1.7014005e+02 - Can anybody suggest what changes I can make The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests 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] gromacs installation on Vista
I would like to know if I can install gromax on vista and the procedure. Thanks Regards, Maryam -- 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
