[gmx-users] remd :Step 1000002 Warning: pressure scaling more than 1%, mu: 333821 333821 333821
dear teacher, when i do remd in the npt ensemble. =md.mdp=== ; Start time and timestep in ps tinit= 0 dt = 0.01 nsteps = 5000 ; For exact run continuation or redoing part of a run ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc_grps = system ; Time constant (ps) and reference temperature (K) tau_t= 0.3 ref_t= 800 ; Pressure coupling Pcoupl = berendsen pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 6.5e-5 ref_p= 1.0 ==error step 00, will finish Mon Nov 28 00:11:22 2011 step 100, will finish Mon Nov 28 00:11:19 2011 Step 102 Warning: pressure scaling more than 1%, mu: 333821 333821 333821 Step 102 Warning: pressure scaling more than 1%, mu: 455440 455440 455440 --- Program mdrun_mpi_4.5.5, VERSION 4.5.5 Source code file: smalloc.c, line: 214 Fatal error: Not enough memory. Failed to realloc -5476105916 bytes for grid-nra, grid-nra=0x38ce0 (called from file nsgrid.c, line 483) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ===command= mpirun n8,8,8,11,11,11,11,2 -np $n_thread /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ ./12/ ./13/ ./14/ ./15/ -replex 50 -nice 0 -s pmma.tpr -o md -c after_md -pd -v log1 how could i do except use the smaller dt or big/small tau_p ? thanks! bodu Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NVT Equilibration
Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The system converged quickly to the reference value (after 2-3ps). Should it converge more slowly and gradually? In the case how could fix it? Thanks-- 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] to gro or not to gro
There is something not quite right here. I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation. I then grompp the original pdb file and run MD to do a single point energy calculation. The values of potential energy values are different by about 3 kJ/mol for a small molecule. These things should carry a bad for your health sign :D -- 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] calculating the pmf in constrained force simulations
Do you mean that you do constrained position simulations and want to know how to process the force? If so, read about thermodynamic integration (TI). I mostly work with US and position restraints, but for absolute constraints I believe that you should take the average force at each constrained position and do a trapezoidal integration of the mean force. Surely somebody has written a paper on this that you can read. Chris. -- original message -- Hi I do constrained force simulations and i have the pullf.xvg and pullx.xvg files.. I want to know how to calculate the force for each simulation and i how to integrate the forces.. can some one help me. -- 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] to gro or not to gro
It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- original message -- There is something not quite right here. I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation. I then grompp the original pdb file and run MD to do a single point energy calculation. The values of potential energy values are different by about 3 kJ/mol for a small molecule. These things should carry a bad for your health sign :D -- 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] Using tables to construct a z-dependent 12-3 potential
Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. Thank you! Olivia -- Olivia Waring Princeton University '12 AB Chemistry -- 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] Using tables to construct a z-dependent 12-3 potential
On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. If you mean z as just one cartesian coordinate you should look into the wall potential options. Otherwise you plot the function in tables as a function of z-z0, since it will be used with the distance. This is in the manual... Thank you! Olivia -- Olivia Waring Princeton University '12 AB Chemistry -- 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] diffusion of the water at the micelle surface
When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this for you. If you don't hear from anybody about how to do this, then I'd suggest that you simply use g_dist to get the time-dependent distance for each water molecule and then use g_traj to output the coordinates of each water molecule and then script it yourself after reading one of the papers where people compute depth-dependent diffusion profiles for a lipid bilayer. Chris. -- original message -- I would like to compute the translational diffusion around the micelle surface. I know that I can select the water molecules at x distance of the micelle surface with g_select (right ?) but how to use this file generated by g_select to compute de diffusion, since the index and/or the number of water will change with the simulation time . Thank you for your response Stephane -- 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] diffusion of the water at the micelle surface
On Sat, Nov 26, 2011 at 11:17 PM, chris.ne...@utoronto.ca wrote: When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this for you. If you don't hear from anybody about how to do this, then I'd suggest that you simply use g_dist to get the time-dependent distance for each water molecule and then use g_traj to output the coordinates of each water molecule and then script it yourself after reading one of the papers where people compute depth-dependent diffusion profiles for a lipid bilayer. Chris. -- original message -- I would like to compute the translational diffusion around the micelle surface. I know that I can select the water molecules at x distance of the micelle surface with g_select (right ?) but how to use this file generated by g_select to compute de diffusion, since the index and/or the number of water will change with the simulation time . You may try g_density, choose different time interval. Thank you for your response Stephane -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww 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] to gro or not to gro
There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- 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] to gro or not to gro
On 2011-11-26 16:38, Igor Druz wrote: There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol the pdb has more decimal digits, hence you have two different sets of coordinates. If you convert the gro back to pdb and the redo the procedure you should get identical numbers. The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca http://utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- 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] to gro or not to gro
There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below). The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file. I see your point, but I don't think it matters. If you really need that precision, then I'd think that you'd be using double precision gromacs (which would still round the output .gro from pdb2gmx and not solve this issue... just saying). gpc-f101n084-$ tail a.gro 2GLYHA2 11 -0.426 0.215 0.193 2GLY C 12 -0.446 0.390 0.072 2GLY O 13 -0.368 0.440 -0.013 3NME N 14 -0.532 0.478 0.154 3NME H 15 -0.618 0.488 0.104 3NMECH3 16 -0.468 0.607 0.173 3NME HH31 17 -0.375 0.594 0.227 3NME HH32 18 -0.533 0.670 0.234 3NME HH33 19 -0.447 0.661 0.081 0.47330 0.80470 0.29640 gpc-f101n084-$ tail a.pdb ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 ATOM 12 C GLY 2 -4.461 3.901 0.720 ATOM 13 O GLY 2 -3.677 4.400 -0.128 HETATM 14 N NME 3 -5.316 4.776 1.535 HETATM 15 H NME 3 -6.182 4.876 1.044 HETATM 16 CH3 NME 3 -4.685 6.072 1.731 HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 END -- original message -- There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- 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] to gro or not to gro
I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. On Sat, Nov 26, 2011 at 3:55 PM, chris.ne...@utoronto.ca wrote: There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below). The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file. I see your point, but I don't think it matters. If you really need that precision, then I'd think that you'd be using double precision gromacs (which would still round the output .gro from pdb2gmx and not solve this issue... just saying). gpc-f101n084-$ tail a.gro 2GLYHA2 11 -0.426 0.215 0.193 2GLY C 12 -0.446 0.390 0.072 2GLY O 13 -0.368 0.440 -0.013 3NME N 14 -0.532 0.478 0.154 3NME H 15 -0.618 0.488 0.104 3NMECH3 16 -0.468 0.607 0.173 3NME HH31 17 -0.375 0.594 0.227 3NME HH32 18 -0.533 0.670 0.234 3NME HH33 19 -0.447 0.661 0.081 0.47330 0.80470 0.29640 gpc-f101n084-$ tail a.pdb ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 ATOM 12 C GLY 2 -4.461 3.901 0.720 ATOM 13 O GLY 2 -3.677 4.400 -0.128 HETATM 14 N NME 3 -5.316 4.776 1.535 HETATM 15 H NME 3 -6.182 4.876 1.044 HETATM 16 CH3 NME 3 -4.685 6.072 1.731 HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 END -- original message -- There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.15997e+02 kJ/mol The mdp file: integrator = md nsteps = 0 nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy= 1 nstxtcout= 0 nstlist = 0 ns_type = simple pbc = no rlist= 0 rcoulomb = 0 rvdw = 0 gen_vel = no unconstrained-start = yes lincs-warnangle = 30 The pdb file : HETATM1 1HH3 ACE 1 -1.449 0.109 -0.581 H HETATM2 CH3 ACE 1 -2.101 -0.268 0.202 C HETATM3 2HH3 ACE 1 -1.708 0.090 1.151 H HETATM4 3HH3 ACE 1 -2.109 -1.350 0.189 H HETATM5 C ACE 1 -3.491 0.269 0.000 C HETATM6 O ACE 1 -4.453 -0.401 -0.152 O ATOM 7 N GLY 2 -3.601 1.734 0.000 N ATOM 8 H GLY 2 -3.039 2.278 -0.623 H ATOM 9 CA GLY 2 -4.525 2.391 0.903 C ATOM 10 HA1 GLY 2 -5.539 2.051 0.696 H ATOM 11 HA2 GLY 2 -4.263 2.147 1.932 H ATOM 12 C GLY 2 -4.461 3.901 0.720 C ATOM 13 O GLY 2 -3.677 4.400 -0.128 O HETATM 14 N NME 3 -5.316 4.776 1.535 N HETATM 15 H NME 3 -6.182 4.876 1.044 H HETATM 16 CH3 NME 3 -4.685 6.072 1.731 C HETATM 17 1HH3 NME 3 -3.754 5.941 2.272 H HETATM 18 2HH3 NME 3 -5.328 6.697 2.341 H HETATM 19 3HH3 NME 3 -4.465 6.615 0.809 H END *In reply to chris.neale at utoronto.ca:* It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] calculating the pmf in constrained force simulations
yes exactly thats what I am trying to do.. Thanks a lot for the suggestion Ramya On Sat, Nov 26, 2011 at 7:26 AM, chris.ne...@utoronto.ca wrote: Do you mean that you do constrained position simulations and want to know how to process the force? If so, read about thermodynamic integration (TI). I mostly work with US and position restraints, but for absolute constraints I believe that you should take the average force at each constrained position and do a trapezoidal integration of the mean force. Surely somebody has written a paper on this that you can read. Chris. -- original message -- Hi I do constrained force simulations and i have the pullf.xvg and pullx.xvg files.. I want to know how to calculate the force for each simulation and i how to integrate the forces.. can some one help me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] to gro or not to gro
1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- 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_clustsize
Dear Prof. I have some problems about g_clustsize program and I didn't find my answer in mailing list. Please help me. I don't know what is the base of selection for -cut option? In my system after doing g_clustsize, when I see nclust.xvg file, it looks like all the atoms in the system were used to find clusters. @ title Number of clusters @ xaxis label Time (ps) @ yaxis label N @TYPE xy 0.00e+00 413 1.50e+02 362 3.00e+02 348 4.50e+02 304 6.00e+02 274 7.50e+02 255 9.00e+02 243 1.05e+03 233 1.20e+03 218 1.35e+03 211 1.50e+03 199 1.65e+03 190 1.80e+03 192 1.95e+03 179 2.10e+03 172 2.25e+03 170 . . . 5.992500e+05 9 5.994000e+05 10 5.995500e+05 9 5.997000e+05 9 5.998500e+05 9 6.00e+05 9 My system consist of 500 monmer. Please help me. Best Regards SARA-- 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] to gro or not to gro
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. You have the option to use pdb or gro or g96. The last format has even more digits, and support for velocities. Pdb has no velocities and gro has lowest precision. All of these are file formats that have not been developed by the gromacs team, but were adopted from other packages. I don't see what kind of warning we should issue when using a gro file, without making it even more confusing. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists 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] g_clustsize
On 2011-11-26 18:55, mohammad agha wrote: Dear Prof. I have some problems about g_clustsize program and I didn't find my answer in mailing list. Please help me. I don't know what is the base of selection for -cut option? In my system after doing g_clustsize, when I see nclust.xvg file, it looks like all the atoms in the system were used to find clusters. that's correct, g_clustsize -h explains it. @ title Number of clusters @ xaxis label Time (ps) @ yaxis label N @TYPE xy 0.00e+00 413 1.50e+02 362 3.00e+02 348 4.50e+02 304 6.00e+02 274 7.50e+02 255 9.00e+02 243 1.05e+03 233 1.20e+03 218 1.35e+03 211 1.50e+03 199 1.65e+03 190 1.80e+03 192 1.95e+03 179 2.10e+03 172 2.25e+03 170 . . . 5.992500e+05 9 5.994000e+05 10 5.995500e+05 9 5.997000e+05 9 5.998500e+05 9 6.00e+05 9 My system consist of 500 monmer. Please help me. Best Regards SARA -- 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] to gro or not to gro
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.neale@utoronto.**ca chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. You have the option to use pdb or gro or g96. The last format has even more digits, and support for velocities. Pdb has no velocities and gro has lowest precision. All of these are file formats that have not been developed by the gromacs team, but were adopted from other packages. I don't see what kind of warning we should issue when using a gro file, without making it even more confusing. it was already in your 1st response: the gro has less decimal digits than pdb when storing coordinates. This should be issued by pdb2gmx. I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] to gro or not to gro
On 2011-11-26 20:15, Igor Druz wrote: On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-11-26 19:07, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca mailto:chris.neale@utoronto.__ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. You have the option to use pdb or gro or g96. The last format has even more digits, and support for velocities. Pdb has no velocities and gro has lowest precision. All of these are file formats that have not been developed by the gromacs team, but were adopted from other packages. I don't see what kind of warning we should issue when using a gro file, without making it even more confusing. it was already in your 1st response: the gro has less decimal digits than pdb when storing coordinates. This should be issued by pdb2gmx. I appreciate the history of the matter, but it would save a lot of headache to store coordinates in angstroms in gro files, i.e., not to omit 2 in 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What is the point in dropping useful 2 by introducing useless 0? History as well. You can have pdb2gmx go straight to g96 (-c conf.g96 will do it) which has higher precision than either of the two others. It is bigger though. As said g96 is also a borrowed format from gromos96. Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists 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 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users
Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential
Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below: title = Alkanethiol SAM MD ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps energygrps = CH3 CH2 S wall0 energygrp_table = CH3 wall0 CH2 wall0 S wall0 ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) coulombtype = Cutoff rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) vdwtype = User rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; Pressure coupling on in NPT ; Periodic boundary conditions pbc = xy; 3-D PBC ; Dispersion correction DispCorr= no; account for cut-off vdW scheme ; Walls nwall = 1 wall_type = table wall_atomtype = wall0 ; Velocity generation gen_vel = no; Velocity generation is off I've defined three energy groups in my system (CH3, CH2, and S), and I have built the following three energy group tables: table_CH3_wall0.xvg table_CH2_wall0.xvg table_S_wall0.xvg I'm not sure whether I should list wall0 among the [ atomtypes ]... When I do, grompp complains about wall0 not being found in the index file. I could add it, but since wall0 doesn't correspond to any actual atoms in my system, I'm not exactly sure how to proceed. In summary, I'm confused as to how to combine the concepts of energy groups and walls when using potential tables. Thank you so much! Olivia On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. If you mean z as just one cartesian coordinate you should look into the wall potential options. Otherwise you plot the function in tables as a function of z-z0, since it will be used with the distance. This is in the manual... Thank you! Olivia -- Olivia Waring Princeton University '12 AB Chemistry -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential
On 2011-11-26 21:01, Olivia Waring wrote: Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below: title = Alkanethiol SAM MD ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps energygrps = CH3 CH2 S wall0 energygrp_table = CH3 wall0 CH2 wall0 S wall0 ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) coulombtype = Cutoff rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) vdwtype = User rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; Pressure coupling on in NPT ; Periodic boundary conditions pbc = xy; 3-D PBC ; Dispersion correction DispCorr= no; account for cut-off vdW scheme ; Walls nwall = 1 wall_type = table wall_atomtype = wall0 ; Velocity generation gen_vel = no; Velocity generation is off I've defined three energy groups in my system (CH3, CH2, and S), and I have built the following three energy group tables: table_CH3_wall0.xvg table_CH2_wall0.xvg table_S_wall0.xvg I'm not sure whether I should list wall0 among the [ atomtypes ]... When I do, grompp complains about wall0 not being found in the index file. I could add it, but since wall0 doesn't correspond to any actual atoms in my system, I'm not exactly sure how to proceed. In summary, I'm confused as to how to combine the concepts of energy groups and walls when using potential tables. I think you have to select a wall_atomtype that is a true atomtype in your force field, since it uses this for the force field parameter. Please check the manual again, I've never used this feature myself, but I would guess that all atoms interact with the wall through the table where a combination rule is used to get the parameters. This could be nonsense though... If all else fail grep for wall in the source code :). Thank you so much! Olivia On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. If you mean z as just one cartesian coordinate you should look into the wall potential options. Otherwise you plot the function in tables as a function of z-z0, since it will be used with the distance. This is in the manual... Thank you! Olivia -- Olivia Waring Princeton University '12 AB Chemistry -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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] Write the total dipole moment on-the-fly?
Dear All, Is there a way to let GROMACS to calculate and write the total dipole moment on-the-fly? I realize that g_dipoles can be used to calculate the total dipole moment using a stored trajectory. However, for a large system it is not very feasible to write the trajectory at a frequency good enough for spectra analysis. Thanks. Hao 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
Re: [gmx-users] to gro or not to gro
On 27/11/2011 5:07 AM, Igor Druz wrote: On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote 1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then I suppose you might need to redo it, but they should be very quick, right? The calculations must be repeated. You are making irrelevant assumptions without knowing what the calculations are for. You asserted that there should have been a warning without explaining why this loss of precision was material. Chris knew that many uses of pdb2gmx change the atomic configuration considerably, e.g. new hydrogen positions, building termini, etc. so that any change of precision of coordinates is not a big deal, and even less important once a simulation has run afterwards. If you want to engage in constructive dialogue, please explain why the loss of precision was material, in order to clarify the reason for your request for a warning message. If you wish to blow off steam, please do it elsewhere. 2. The .gro files do not carry useless zeroes. you have it backwards... the gro files end up with fewer digits. 0.417 or 4.172. Shall I continue? I know which one I prefer. 3. it's a little annoying to find out that you already knew the answer. Why not state that at the outset? Unless I misunderstand this point, this will mark the end of my comments since holding back information on purpose just wastes people's time. Check my 1st e-mail, please. It is NOT asking for clarification. It is requesting an explicit warning message. There's nothing to warn about. You thought that switching from Angstrom to nanometers was significant somehow, and then assumed that different file formats would definitely contain identical information, and didn't check their contents. Mark Chris. -- original message -- I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the bad for the health sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros. -- gmx-users mailing list gmx-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 thewww 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT Equilibration
Alex Jemulin wrote: Dear all I'm studying a membrane protein. I've run equilibration with the follwing parameters - reference temperature =323k integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs tcoupl = V-rescale ; modified Berendsen thermostat The system converged quickly to the reference value (after 2-3ps). Should it converge more slowly and gradually? In the case how could fix it? It should likely converge very quickly. I see nothing wrong. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_clustsize
Dear Prof. Spoel Thank you very much for your reply, but I don't understand what I want! In the g_clustsize there is only -cut = Largest distance (nm) to be considered in a cluster between my questions and I don't know the base of selection for -cut. I practice different numbers for -cut and took different results but may I know the most exact number for it? Best Regards Sara From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, November 26, 2011 10:09 PM Subject: Re: [gmx-users] g_clustsize On 2011-11-26 18:55, mohammad agha wrote: Dear Prof. I have some problems about g_clustsize program and I didn't find my answer in mailing list. Please help me. I don't know what is the base of selection for -cut option? In my system after doing g_clustsize, when I see nclust.xvg file, it looks like all the atoms in the system were used to find clusters. that's correct, g_clustsize -h explains it. @ title Number of clusters @ xaxis label Time (ps) @ yaxis label N @TYPE xy 0.00e+00 413 1.50e+02 362 3.00e+02 348 4.50e+02 304 6.00e+02 274 7.50e+02 255 9.00e+02 243 1.05e+03 233 1.20e+03 218 1.35e+03 211 1.50e+03 199 1.65e+03 190 1.80e+03 192 1.95e+03 179 2.10e+03 172 2.25e+03 170 . . . 5.992500e+05 9 5.994000e+05 10 5.995500e+05 9 5.997000e+05 9 5.998500e+05 9 6.00e+05 9 My system consist of 500 monmer. Please help me. Best Regards SARA -- 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.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] editconf -d
Dear Prof. I have a system consists of 500 surfactants + 61000 water beads + 500 ion in martini force field into cubic box with 20.3*20.3*20.3 dimensions, May I know the best quantity for -d option in editconf program to prevent from artificial forces, please? Best Regards Sara -- 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
