Re: [gmx-users] removing pbc jumps from trajectory
You have to make sure of two things: 1- use a reference (gro or tpr) where the molecule is whole! The tpr is prefered since the molecules are defined. 2- with such a reference and the option -mol you'll get a trajectory with the protein as a whole. On that trajectory you may apply more modifications: -nojump with generate a trajectory where the pbc are not applied so you can do msd analysis. Note that thisnis done by default in g_msd. - fitting with only translation removed (equivalent to centering but more stable. Centering works strangely) XAvier. On Feb 21, 2011, at 8:52, Evelyne Deplazes depla...@student.uwa.edu.au wrote: Hi I have a series of trajectories from a coarse grained simulation (Martini force field) that I ran using gromacs 4.0.4. The system consists of a protein embedded in a POPC bilayer solvated with water. During the simulation the protein (most of time its actually *part* of the protein) jumps across the pb into the neighboring box. I use a series of tcl scripts to analyse my trajectories and for that purpose I need to remove that period boundary jump and make the protein whole again. I have tried the approach described on the gromacs website http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions I also other combinations of -whole, -center and -pbc nojump of trjconv, without any luck. Can anyone suggest how I can re-center the protein and remove the pb jump ie make the protein whole Thanks Evelyne -- Evelyne Deplazes PhD student Theoretical Chemistry group University of Western Australia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
I tried a couple of things according to your suggestions, but no luck so far I used the following commands 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc no luck...If I use command 1) only the trajout_mol.xtc the protein is still split into to across 2 boxes ie it looks like it did not do anything to the trajectory if I use 1) and 2) the system gets ripped apart. The system is no longer a box but a flat disk (very funky) then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit translation -o trajout_fit.xtc again...it looks like the trajectory did not change and the protein is still jumping out of the box then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -trans -6 6 0 -o trajout_trans.xtc(the box is about 12 x 12) now at least this command did something to the trajectory. The entire protein is now in the center of the box (rather than in the corner) but in the frames where the pb jump occurs the protein still jumps out of the box! it now simply jumps from the center to the next box rather than sliding across the border into the next box On 21 February 2011 16:02, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar) 2. Re: g_covar to calculate correlation of motion (bipin singh) 3. removing pbc jumps from trajectory (Evelyne Deplazes) 4. Re: removing pbc jumps from trajectory (XAvier Periole) -- Forwarded message -- From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 21 Feb 2011 08:14:26 +0100 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- * - Thanks and regards Bipin Singh * * * -- 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 -- Forwarded message -- From: bipin singh bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 21 Feb 2011 13:17:48 +0530 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has47 elements Group 2 ( HIS) has86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has 190 elements Group 9 ( ALA) has 110 elements Group10 ( SER) has 143 elements Group11 ( PHE) has80 elements Group12 ( LYS) has 242 elements Group13 ( TYR) has 189 elements Group14 ( LEU) has 304 elements Group15 ( GLN) has 102 elements Group16 ( TRP) has48 elements Group17 (
Re: [gmx-users] configure: error: cannot compute sizeof (off_t)
On Feb 20, 2011, at 9:30 PM, Justin Kat wrote: Dear experts, I am still unable to overcome this error during the configuration: configure: error: cannot compute sizeof (off_t) See `config.log' for more details. So what does config.log say about cannot compute sizeof (off_t) ? Carsten I came across this thread with the exact same setup as I have: http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html I have tried uninstalling openmpi 1.4.4 and installing the more stable openmpi1.4.3 but I am still experiencing the same error. ./configure --enable-mpi --program-suffix=_mpi MPICC=/usr/local/bin/mpicc --with-fft=fftw3 I have also tried to explicitly provide the path to mpicc as above but it still gives me the same error. This may or may not be relevant but at the end of the config.log there is also this line: configure: exit 77 Does that mean anything? Any help at all is appreciated! Thanks, 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
ok this does not make sense! Did you check your tpr file? the command 1) should give you a trajectory where the molecules are whole but jumping across the boundaries ... if it does not that means that the tpr is fucky! Try to visualize your tpr in vmd ... night give you some insight on what is going on! You could also make a tpr file ... making sure things a fine :)) On Feb 21, 2011, at 9:45 AM, Evelyne Deplazes wrote: I tried a couple of things according to your suggestions, but no luck so far I used the following commands 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc no luck...If I use command 1) only the trajout_mol.xtc the protein is still split into to across 2 boxes ie it looks like it did not do anything to the trajectory if I use 1) and 2) the system gets ripped apart. The system is no longer a box but a flat disk (very funky) then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit translation -o trajout_fit.xtc again...it looks like the trajectory did not change and the protein is still jumping out of the box then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -trans -6 6 0 - o trajout_trans.xtc(the box is about 12 x 12) now at least this command did something to the trajectory. The entire protein is now in the center of the box (rather than in the corner) but in the frames where the pb jump occurs the protein still jumps out of the box! it now simply jumps from the center to the next box rather than sliding across the border into the next box On 21 February 2011 16:02, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar) 2. Re: g_covar to calculate correlation of motion (bipin singh) 3. removing pbc jumps from trajectory (Evelyne Deplazes) 4. Re: removing pbc jumps from trajectory (XAvier Periole) -- Forwarded message -- From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 21 Feb 2011 08:14:26 +0100 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- - Thanks and regards Bipin Singh -- 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 -- Forwarded message -- From: bipin singh bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 21 Feb 2011 13:17:48 +0530 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has47 elements Group 2 ( HIS) has86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has
Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
Hi Evelyne, 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc The option -pbc mol IIRC relates to the option for the unit cell representation (-ur). To unbreak molecules using trjconv, you need to have .tpr file and use the option -pbc whole. 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc if I use 1) and 2) the system gets ripped apart. The system is no longer a box but a flat disk (very funky) This is because the jumps are removed and over time the lipids diffuse in the plane. They've diffused quite a bit probably, smearing themselves out over a disk. Groetjes, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_covar to calculate correlation of motion
Hi Bipin, The file residuetypes.dat is quite different from aminoacids.dat. You can paste the following into that file (first line is number of entries, followed by so many residue names): 49 ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA GLN GLU GLUH GLY HIS HIS1 HISA HISB HISH HYP ILE LEU LYS LYSH MELEU MET MEVAL NAC NH2 PHE PHEH PHEU PHL PRO SER THR TRP TRPH TRPU TYR TYRH TYRU VAL Groetjes, Tsjerk On Mon, Feb 21, 2011 at 8:47 AM, bipin singh bipinel...@gmail.com wrote: Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has 47 elements Group 2 ( HIS) has 86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has 56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has 68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has 190 elements Group 9 ( ALA) has 110 elements Group 10 ( SER) has 143 elements Group 11 ( PHE) has 80 elements Group 12 ( LYS) has 242 elements Group 13 ( TYR) has 189 elements Group 14 ( LEU) has 304 elements Group 15 ( GLN) has 102 elements Group 16 ( TRP) has 48 elements Group 17 ( ARG) has 120 elements Group 18 ( ASP) has 108 elements Group 19 ( THR) has 141 elements Group 20 ( SOL) has 27882 elements Group 21 ( CL) has 5 elements On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- - Thanks and regards Bipin Singh -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-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 -- - Thanks and regards Bipin Singh -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_covar to calculate correlation of motion
Thanks a lot Sir. On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, The file residuetypes.dat is quite different from aminoacids.dat. You can paste the following into that file (first line is number of entries, followed by so many residue names): 49 ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA GLN GLU GLUH GLY HIS HIS1 HISA HISB HISH HYP ILE LEU LYS LYSH MELEU MET MEVAL NAC NH2 PHE PHEH PHEU PHL PRO SER THR TRP TRPH TRPU TYR TYRH TYRU VAL Groetjes, Tsjerk On Mon, Feb 21, 2011 at 8:47 AM, bipin singh bipinel...@gmail.com wrote: Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has47 elements Group 2 ( HIS) has86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has 190 elements Group 9 ( ALA) has 110 elements Group10 ( SER) has 143 elements Group11 ( PHE) has80 elements Group12 ( LYS) has 242 elements Group13 ( TYR) has 189 elements Group14 ( LEU) has 304 elements Group15 ( GLN) has 102 elements Group16 ( TRP) has48 elements Group17 ( ARG) has 120 elements Group18 ( ASP) has 108 elements Group19 ( THR) has 141 elements Group20 ( SOL) has 27882 elements Group21 ( CL) has 5 elements On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- - Thanks and regards Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- - Thanks and regards Bipin Singh -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how many contacts has a certain atom at MD
Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how many contacts has a certain atom at MD
g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how many contacts has a certain atom at MD
Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at the moment. Version 4.0.x seem to work better. XAvier Periole skrev 2011-02-21 11.37: g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- 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 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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] how many contacts has a certain atom at MD
g_mindist -on (with suitable index groups) should also do the trick. -Justin Erik Marklund wrote: Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at the moment. Version 4.0.x seem to work better. XAvier Periole skrev 2011-02-21 11.37: g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how many contacts has a certain atom at MD
Thank you very much. best, Olga 2011/2/21 Justin A. Lemkul jalem...@vt.edu g_mindist -on (with suitable index groups) should also do the trick. -Justin Erik Marklund wrote: Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at the moment. Version 4.0.x seem to work better. XAvier Periole skrev 2011-02-21 11.37: g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Porting Amber parmbsc0 force field to Gromacs
Hello, gods of gromacs, I have ported the parmbsc0 modifications to a new gromacs force field, based on the amber99sb.ff, this involves adding a new carbon atom (CI) to be used in the C5' of nucleotides. Everything is working perfectly (to my astonishment) and I am confident of all of the modifications I have made, except for the func column in [diheadraltypes]. The only way I can get the parameters that involve the same four atoms to work is to alter this column. I have read chapter 5 but I cannot see in what way this will affect the new ff. These are the original parameters from AMBERparmbsc0: DIHE X -CI-OS-X 3 1.150 0.0 3.0 X -CI-OH-X 3 0.500 0.0 3.0 X -CI-CT-X 9 1.400 0.0 3.0 CT-OS-CT-CI1 0.383 0.0-3.0 CT-OS-CT-CI1 0.100 180.0 2.0 H1-CI-CT-OS1 0.250 0.0 1.0 H1-CI-CT-OH1 0.250 0.0 1.0 H1-CT-CI-OS1 0.250 0.0 1.0 H1-CT-CI-OH1 0.250 0.0 1.0 CI-CT-CT-CT1 0.180 0.0-3.0 CI-CT-CT-CT1 0.250 180.0-2.0 CI-CT-CT-CT1 0.200 180.0 1.0 OS-P -OS-CI1 0.185181 31.79508-1.0 alfa OS-P -OS-CI1 1.256531 351.95960-2.0 alfa OS-P -OS-CI1 0.354858 357.24748 3.0 alfa OH-P -OS-CI1 0.185181 31.79508-1.0 alfa OH-P -OS-CI1 1.256531 351.95960-2.0 alfa OH-P -OS-CI1 0.354858 357.24748 3.0 alfa CT-CT-CI-OS1 1.178040 190.97653-1.0 gamma CT-CT-CI-OS1 0.092102 295.63279-2.0 gamma CT-CT-CI-OS1 0.962830 348.09535 3.0 gamma CT-CT-CI-OH1 1.178040 190.97653-1.0 gamma CT-CT-CI-OH1 0.092102 295.63279-2.0 gamma CT-CT-CI-OH1 0.962830 348.09535 3.0 gamma This is from my amberbsc0/ffbonded.itp: ;i j k l func phase kd pn CT OS CT CI40.00 0.38300-3; parmbsc0 Will Stebbeds CT OS CT CI4 180.00 0.1 2; parmbsc0 Will Stebbeds H1 CI CT OS40.00 0.25000 1; parmbsc0 Will Stebbeds H1 CI CT OH 40.00 0.25000 1; parmbsc0 Will Stebbeds H1 CT CI OH 40.00 0.25000 1; parmbsc0 Will Stebbeds CI CT CT CT40.00 0.18000-3; parmbsc0 Will Stebbeds CI CT CT CT4 180.00 0.25000-2; parmbsc0 Will Stebbeds CI CT CT CT4 180.00 0.2 1; parmbsc0 Will Stebbeds OS P OS CI4 31.79 0.18518-1; parmbsc0 Will Stebbeds OS P OS CI4 351.96 1.25653-2; parmbsc0 Will Stebbeds OS P OS CI4 357.25 0.35486 3; parmbsc0 Will Stebbeds OH P OS CI4 31.79 0.18518-1; parmbsc0 Will Stebbeds OH P OS CI4 351.96 1.25653-2; parmbsc0 Will Stebbeds OH P OS CI4 357.25 0.35486 3; parmbsc0 Will Stebbeds CT CT CI OS4 190.98 1.17804-1; parmbsc0 Will Stebbeds CT CT CI OS4 295.63 0.09210-2; parmbsc0 Will Stebbeds CT CT CI OS4 348.09 0.96283 3; parmbsc0 Will Stebbeds CT CT CI OH 4 190.98 1.17804-1; parmbsc0 Will Stebbeds CT CT CI OH 4 295.63 0.09210-2; parmbsc0 Will Stebbeds CT CT CI OH 4 348.10 0.96283 3; parmbsc0 Will Stebbeds ;i j k l func X CI OS X 9 0.0 1.15000 3 ; parmbsc0 Will Stebbeds X CI OH X 9 0.0 0.5 3 ; parmbsc0 Will Stebbeds X CI CT X 9 0.0 1.4 3 ; PARMBSC0 --- Will Stebbeds As you can see func=1 was changed to func=4 and func=3 was changed to func=9. This was the only way I could find in which the parameters would work, is it valid to make such alterations arbitrarily? The only other way it will work is if I comment out the repeated lines for the same 4 atoms. Any help on this matter would be very much appreciated. best regards Will Date: Sat, 5 Feb 2011 12:23:32 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Porting Amber parmbsc0 force field to Gromacs william Stebbeds wrote: Hello, I would like to use the parmbs0 Amber forcefield to Gromacs, specifically the nucleic acid parameters. Is this likely to come in a future release? Force fields are only implemented if a developer has a compelling reason to do so, and then take the time to validate it. As such, new force fields are not often introduced. I appreciate that this
Re: [gmx-users] how many contacts has a certain atom at MD
So I used mindist for a certain group of molecules which is surrounded by water. I got plot number of contacts versuc sumulation time. According to what I see in a distance 0.6nm at certain frame there are on average 150 contacts. Actually how the programm calculates the number of contacts, if someone knows what is a creteria that a certain contact is formed? Is is a certain distance. best, Olga 2011/2/21 Olga Ivchenko olga.ivche...@gmail.com Thank you very much. best, Olga 2011/2/21 Justin A. Lemkul jalem...@vt.edu g_mindist -on (with suitable index groups) should also do the trick. -Justin Erik Marklund wrote: Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at the moment. Version 4.0.x seem to work better. XAvier Periole skrev 2011-02-21 11.37: g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how many contacts has a certain atom at MD
Olga Ivchenko wrote: So I used mindist for a certain group of molecules which is surrounded by water. I got plot number of contacts versuc sumulation time. According to what I see in a distance 0.6nm at certain frame there are on average 150 contacts. Actually how the programm calculates the number of contacts, if someone knows what is a creteria that a certain contact is formed? Is is a certain distance. Exactly as the title of the output says, a contact exists if any two atoms of the chosen index groups are within 0.6 nm. You can change the distance with g_mindist -d. -Justin best, Olga 2011/2/21 Olga Ivchenko olga.ivche...@gmail.com mailto:olga.ivche...@gmail.com Thank you very much. best, Olga 2011/2/21 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu g_mindist -on (with suitable index groups) should also do the trick. -Justin Erik Marklund wrote: Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at the moment. Version 4.0.x seem to work better. XAvier Periole skrev 2011-02-21 11.37: g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Target implementation date for gb_saltconc?
Skickat från min iPhone 18 feb 2011 kl. 21:10 skrev Matthew Zwier mczw...@gmail.com: Dear GROMACS developers and users, Our research group is interested in performing GBSA simulations with GROMACS, but we would need to perform them with a nonzero salt concentration. I was wondering if there are plans to implement the gb_saltconc parameter, and if so, when it might become available. Many thanks, Matt Zwier University of Pittsburgh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] free energy-couple-intramol options
Hello, I read through the couple-intramol options (yes and no) good many times but I can not still realize what is the difference and which option I should select. I am having a hydrocarbon system (polyethylene in hexane as solvent). Can anyone help me understand these options please? (in plain english) option yes, says something about FF of large molecules which is my case...but I dont see the statement: nb interactions might lead to kinetically trapped vaccum conformations?! Also, as with the electrostatics treatment in my hydrocarbon system I am still unsure if I need to include electrostatics potentials. I digged into the literature and found the following articles containing nonpolar polymers where vdw is the only nonbonded term in the FF. http://pubs.acs.org/doi/abs/10.1021/ma9600419 http://www.sciencedirect.com/science?_ob=ArticleURL_udi=B6TXW-40TY56F-16_user=458507_coverDate=11%2F30%2F2000_rdoc=1_fmt=high_orig=search_origin=search_sort=d_docanchor=view=c_searchStrId=1650178009_rerunOrigin=google_acct=C22002_version=1_urlVersion=0_userid=458507md5=bf0b74cfc76e0dafbadf06396fb63745searchtype=a Please let me know your comments Thanks Moeed -- 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 constant
Hello, I am trying to calculate the diffusion coefficient of a molecule in water using g_msd, and I have a doubt: I get 3 different values when I use the trajectory directly from the simulation, the trajectory using PBC conditions, and the fitted trajectory. Which would be the correct value for the diffusion coefficient? Thanks a lot for your help in advance. Best wishes, Rebeca Garcia Organic Chemistry Department Santiago de Compostela University Spain -- 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] PMF from pull code, unexpected results
Dear all, I would like to calculate the potential of mean force between two molecules in aqueous solution using the pull code. For a start i performed a number of calulations with a couple of very simple model systems with settings loosely based on the example in the gmx tutorial section (see mdp file included at the bottom). My box is 8x8x8 nm**3, pmf is calculated from some r_min up to approx 3.8 nm. Performing simulations with two t-buntanol molecules in implicit solvent, anlyzing the output (x and f*.xvg files) with g_wham, i get rather unexpected results: The PMFs look very differnt depending on whether I use pulldim Y Y Y or pulldim N N Y: http://www.brunsteiner.net/tbut-pmf.gif Since we look at two neutral molecules with a permanent dipole moment one would expect the PMF to be negative up to a distance at which the two molecules come into contact, but with pulldim Y Y Y the PMF is positive, i.e., repulsive, throughout. With pulldim N N Y I constrain the two molecules in two dimensions (by freezing the central atom in the x and y dimensions only, BTW any ideas how else i could achieve that?) One could argue that a combination of frozen atoms and pull code might be problematic, but i freeze and pull in different dimensions, so this should be OK, and, more importantly: with pulldim N N Y i get results that look much more reasonable than with pulldim Y Y Y and NO additional constraints. With pulldim Y Y Y the RDF (option nolog in g_wahm) looks, in fact, like a NON-normalized rdf: http://www.brunsteiner.net/tbut-rdf.gif and, interestingly if i normalize it myself (by dividing through z**2 before taking the logarithm) the resulting PMF looks much more reasonable. Although what I see suggests that with pulldim Y Y Y the RDF just doesn't normalized properly, this issue seems to be more involved: Looking at the average forces and positions (the content of the f*xvg and x*xvg files) http://www.brunsteiner.net/tbut-f.gif http://www.brunsteiner.net/tbut-z.gif suggests that there's already something wrong in the mdrun output meaning that the problem is further upstream and not connected to anything done by g_wham. I repeated the calculations with an even simpler system (2 single atoms that only interact via a LJ potential) to get qualitatively the same results: http://www.brunsteiner.net/2at-pmf.gif http://www.brunsteiner.net/2at-rdf.gif http://www.brunsteiner.net/2at-z.gif http://www.brunsteiner.net/2at-f.gif A few more remarks: 1) Convergence does not seem to be an issue here as i extended some of the calculations to include 35+ windows, 2 ns each, and the PMF remains the same nearly quantitatively. 2) The length of my reaction coordinates is always shorter than half the box length. 3) I've compared calculations cut-off vs PME, to get very similar results. 4) If I use pulldim Y Y Y with no additional constraints but with comm_mode = Angular i get results somewhere inbetween the two cases above. my specs: Gromacs version: 4.5.3 Linux 2.6.35-23-generic Ubuntu x86_64 gcc version 4.4.5 I am not sure whether i overlooked something in my input, or whether there's a problem with code. I'd be grateful for any ideas/suggestions! cheers, Michael = mdp file: integrator = sd; this is better than md/NHT for systems with very few DOFs tau_t = 2.0 2.0 ref_t = 290 290 ; a bit lower than 298 since sd with default parameters ; has problems controlling the temperature. tc_grps = p1 p2 ; also tried System here, no difference ; dt = 0.002 tinit = 0 nsteps = 10; played with that, results seem to have converged nstxout = 1000 nstvout = 0 nstfout = 1000 nstenergy = 100 ; constraint_algorithm = lincs constraints = hbonds continuation = no ; comm_mode = Linear nstcomm = 1 pbc = xyz ; also tried pbc = no same result nstlist = 10 ns_type = grid rlist = 4.0 rcoulomb= 4.0 rvdw= 4.0 ; coulombtype = Shift vdwtype = Shift epsilon_r = 80 ; pull= umbrella pull_geometry = distance pull_dim= N N Y ; or Y Y Y pull_start = yes pull_ngroups= 1 pull_group0 = p1 pull_group1 = p2 pull_rate1 = 0.0 pull_k1 = 500 ; i let this number vary depending on the pull distance; ; also played with the numbers, same result pull_nstxout= 100 pull_nstfout= 100 pull_pbcatom0 = 1 ; my system geometry is so that the molecules never leave the box pull_pbcatom1 = 16 ; or cross a cell boundary. ; freezegrps = c1 c2; with pulldim Y Y Y these lines are freezedim = Y Y N Y Y N ; removed or commented out ; energygrps = p1 p2 -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] An argument about long range electrostatics
Hassan Shallal wrote: Dear Gromacs users, While I was using Gromos force field in simulating a protein in explicit solvent, I used the following parameters: *rcoulomb = 1, rlist =1, rvdw = 1.4* *Electrostatitcs : PME* *VDW : Twin range cutoff* The above situation will not allow the calculation of any *long-range electrostatics (LR-Coul)* while calculating the energy of interaction among the specified energy groups of the the studied system. Actually, you're calculating lots of long-range electrostatic interactions, but with PME it is the reciprocal space term, Coul-recip. I am facing the question of to what extent that could affect the accuracy of the calculation of the energy of interaction among the specified energy groups of the the studied system. I argue that electrostatic interaction is mainly composed of H-bonds and salt-bridges, both with distance cutoffs of 0.35 nm and 0.4 nm respectively. So there should not be any need for calculating any electrostatic interaction beyond 1 nm (rcoulomb). If you maintain that all Coulombic interactions occur within 0.4 nm, why arbitrarily set a 1-nm cutoff? By that logic, anything beyond 0.4 nm is unimportant. Therein lies the flaw. Electrostatic interactions decay over a longer range than do other interactions like van der Waals forces. If an interaction at 1.0 nm is worth calculating, why is one at 1.001 nm completely unimportant? Simple truncation leads to notable artifacts, which have been documented in the literature. The first paragraph of the 1995 PME paper describes several. On the other hand, I came across another argument that calculating the long range electrostatics is *complicated by the practical limitations of dividing lattice sum energies into energy groups*. I could not find any explanation of this point in the Gromacs manual! But I assume this kind of argument could be valid if ignoring the long range electrostatics would drastically affect the accuracy of interaction energy calculations mentioned above. The manual is not a complete repository of all knowledge, but in conjunction with the 140 or so references therein, it comes pretty close ;) The mesh term in the PME calculation cannot be decomposed pairwise, that much is true. But the effects on the dynamics of the system when not calculating long-range electrostatics (i.e. plain cutoffs) is what is very troubling. By all means, if you want to use the pinnacle of 1980's methodology, use a plain cutoff :) In any case, the counterargument to yours played out in the literature long ago. As I said, within the first few lines of the 1995 PME paper, you'll find lots of reasons to use a long-range electrostatics method. There are several recent demonstrations that PME is the most accurate for a variety of systems. -Justin I would appreciate any feedback or comment concerning the above arguments. Thanks a lot Hassan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] An argument about long range electrostatics
Dear Gromacs users, While I was using Gromos force field in simulating a protein in explicit solvent, I used the following parameters: rcoulomb = 1, rlist =1, rvdw = 1.4 Electrostatitcs : PME VDW : Twin range cutoff The above situation will not allow the calculation of any long-range electrostatics (LR-Coul) while calculating the energy of interaction among the specified energy groups of the the studied system. I am facing the question of to what extent that could affect the accuracy of the calculation of the energy of interaction among the specified energy groups of the the studied system. I argue that electrostatic interaction is mainly composed of H-bonds and salt-bridges, both with distance cutoffs of 0.35 nm and 0.4 nm respectively. So there should not be any need for calculating any electrostatic interaction beyond 1 nm (rcoulomb). On the other hand, I came across another argument that calculating the long range electrostatics is complicated by the practical limitations of dividing lattice sum energies into energy groups. I could not find any explanation of this point in the Gromacs manual! But I assume this kind of argument could be valid if ignoring the long range electrostatics would drastically affect the accuracy of interaction energy calculations mentioned above. I would appreciate any feedback or comment concerning the above arguments. Thanks a lot Hassan -- 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] Can g_wham support using different temperature for different windows?
Jianguo Li wrote: Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows? If g_wham cannot deal with the bias due to using different T, I may need to do REMD in those windows. But that will be very expensive computationally. Anybody have an idea of enhancing sampling in those windows? Btw, I am using Martini CG model. Any suggestions will be highly appreciated, thank you! A more straightforward approach is to (1) add more sampling windows or (2) increase the force constant in regions where there's poor sampling, or perhaps both. -Justin Cheers, Jianguo -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can g_wham support using different temperature for different windows?
Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows? If g_wham cannot deal with the bias due to using different T, I may need to do REMD in those windows. But that will be very expensive computationally. Anybody have an idea of enhancing sampling in those windows? Btw, I am using Martini CG model. Any suggestions will be highly appreciated, thank you! Cheers, Jianguo -- 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] Can g_wham support using different temperature for different windows?
Jianguo Li wrote: Thanks Justin. I tried your suggestions by either increase more windows and change the force constant, but it seems the samplings are still bad in some windows. When I did pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got different configurations at certain reaction coordinates. And the windowed umbrella sampling seems depends strongly on the initial configurations in that window. Therefore I got different PMFs using pulling in (0 0 1) direction and reverse pulling in （0 0 -1) direction. How long are each of the simulations in each window? Sufficient sampling should eliminate any configurational bias and/or hysteresis. Also, if the pulling that sets up the initial configurations is done slowly enough, you won't see these problems. Sounds to me like you're pulling too fast or hard, such that the system is not stable. In my simulation, I exert constraints on phosphate atoms in z direction, so there is no lipid flip-flop and the membrane will be stable at high temperatures. Then I am thinking of increasing temperature in those bad windows to enhance sampling... I don't know if I can make a convincing argument here, but intuitively, these windows would be sampling in a different ensemble, so the free energy landscape in these windows would be discontinuous with any adjacent windows that are done at different temperatures, and perhaps the forces required to restrain your peptide at a given COM distance will still result in a discontinuous PMF. I would also suspect that g_wham can't handle this situation; it has a -temp flag, but it only takes one value. So if you construct your PMF curve using WHAM, but supply incorrect or inconsistent information, I certainly wouldn't believe the result. I guess the main point is, there are tons of published demonstrations of peptides and other molecules crossing a membrane with SMD and umbrella sampling, so it should be possible to generate stable configurations without any funny tricks. -Justin best regards, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, 22 February 2011 09:35:37 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows? If g_wham cannot deal with the bias due to using different T, I may need to do REMD in those windows. But that will be very expensive computationally. Anybody have an idea of enhancing sampling in those windows? Btw, I am using Martini CG model. Any suggestions will be highly appreciated, thank you! A more straightforward approach is to (1) add more sampling windows or (2) increase the force constant in regions where there's poor sampling, or perhaps both. -Justin Cheers, Jianguo -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
[gmx-users] ffamber03 RB dihedrals and amb2gmx.pl problem!
Hello all I obtained a top file after running the amb2gmx.pl script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that with the Ryckaert-Bellemans potential the 1-4 interactions must be excluded from the non-bonded list. So I think this top file is incorrect? Force field is amber03 in gmx4.5.1,ligand is disaccharide. 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] PMF from pull code, unexpected results
Looking at http://www.brunsteiner.net/tbut-pmf.gif you seem to be getting exactly what I would expect. The difference is the entropy term. Note that the spherical shell increases volume as r increases for pulldim YYY but this effect is absent for pulldim NNY. This is why you can correct as per an RDF. Please note that I didn;t check everything thoroughly or look at the other images so there could still be something weird going on, but I disagree that http://www.brunsteiner.net/tbut-pmf.gif shows anything strange. Chris. -- original message -- Dear all, I would like to calculate the potential of mean force between two molecules in aqueous solution using the pull code. For a start i performed a number of calulations with a couple of very simple model systems with settings loosely based on the example in the gmx tutorial section (see mdp file included at the bottom). My box is 8x8x8 nm**3, pmf is calculated from some r_min up to approx 3.8 nm. Performing simulations with two t-buntanol molecules in implicit solvent, anlyzing the output (x and f*.xvg files) with g_wham, i get rather unexpected results: The PMFs look very differnt depending on whether I use pulldim Y Y Y or pulldim N N Y: http://www.brunsteiner.net/tbut-pmf.gif Since we look at two neutral molecules with a permanent dipole moment one would expect the PMF to be negative up to a distance at which the two molecules come into contact, but with pulldim Y Y Y the PMF is positive, i.e., repulsive, throughout. With pulldim N N Y I constrain the two molecules in two dimensions (by freezing the central atom in the x and y dimensions only, BTW any ideas how else i could achieve that?) One could argue that a combination of frozen atoms and pull code might be problematic, but i freeze and pull in different dimensions, so this should be OK, and, more importantly: with pulldim N N Y i get results that look much more reasonable than with pulldim Y Y Y and NO additional constraints. With pulldim Y Y Y the RDF (option nolog in g_wahm) looks, in fact, like a NON-normalized rdf: http://www.brunsteiner.net/tbut-rdf.gif and, interestingly if i normalize it myself (by dividing through z**2 before taking the logarithm) the resulting PMF looks much more reasonable. Although what I see suggests that with pulldim Y Y Y the RDF just doesn't normalized properly, this issue seems to be more involved: Looking at the average forces and positions (the content of the f*xvg and x*xvg files) http://www.brunsteiner.net/tbut-f.gif http://www.brunsteiner.net/tbut-z.gif suggests that there's already something wrong in the mdrun output meaning that the problem is further upstream and not connected to anything done by g_wham. I repeated the calculations with an even simpler system (2 single atoms that only interact via a LJ potential) to get qualitatively the same results: http://www.brunsteiner.net/2at-pmf.gif http://www.brunsteiner.net/2at-rdf.gif http://www.brunsteiner.net/2at-z.gif http://www.brunsteiner.net/2at-f.gif A few more remarks: 1) Convergence does not seem to be an issue here as i extended some of the calculations to include 35+ windows, 2 ns each, and the PMF remains the same nearly quantitatively. 2) The length of my reaction coordinates is always shorter than half the box length. 3) I've compared calculations cut-off vs PME, to get very similar results. 4) If I use pulldim Y Y Y with no additional constraints but with comm_mode = Angular i get results somewhere inbetween the two cases above. my specs: Gromacs version: 4.5.3 Linux 2.6.35-23-generic Ubuntu x86_64 gcc version 4.4.5 I am not sure whether i overlooked something in my input, or whether there's a problem with code. I'd be grateful for any ideas/suggestions! cheers, Michael = mdp file: integrator = sd; this is better than md/NHT for systems with very few DOFs tau_t = 2.0 2.0 ref_t = 290 290 ; a bit lower than 298 since sd with default parameters ; has problems controlling the temperature. tc_grps = p1 p2 ; also tried System here, no difference ; dt = 0.002 tinit = 0 nsteps = 10; played with that, results seem to have converged nstxout = 1000 nstvout = 0 nstfout = 1000 nstenergy = 100 ; constraint_algorithm = lincs constraints = hbonds continuation = no ; comm_mode = Linear nstcomm = 1 pbc = xyz ; also tried pbc = no same result nstlist = 10 ns_type = grid rlist = 4.0 rcoulomb= 4.0 rvdw= 4.0 ; coulombtype = Shift vdwtype = Shift epsilon_r = 80 ; pull= umbrella pull_geometry = distance pull_dim= N N Y ; or Y Y Y pull_start = yes pull_ngroups= 1 pull_group0 = p1 pull_group1 = p2 pull_rate1 = 0.0 pull_k1 = 500 ; i let this number
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Thanks for your comments, Justin. Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time. The pulling rate is 0.001 nm/ps. Is it too fast? My system is a little different. My peptide is highly positively charged. The NMR experiments show that the conformation of the peptide in water is very dynamic, so I make it flexible without fixing any secondary structure in Martini model. In the membrane, 25% of the lipids are negatively charged, so there are very strong electrostatic attraction between peptides and membrane. During the peptide approaching the membrane from the top, peptide can take different configurations at different reaction coordinates. When pulling the peptide into the membrane, the peptide takes relatively compact structure and interacts with only the top leaflet until the distance becomes smaller than 0.45 nm, after that the peptide becomes extended structure and interacts with both leaflets. This extended structure remains until the distance becomes -1.05 nm. Further pulling leads to compact structure and interacts only with the lower leaflet. So the comformation of the peptide is not symmetric between the center of the bilayer, which leads to Hysteresis. It seems that there is a huge energy barrier for the peptide to translocate across the membrane because if the initial conformation in a certain window is extended (interacting with both leaflets), then it remains extended. Similarly, it the initial conformation in a certain window is compact (interacting with only one leaflet), it will remain compact. Any Suggestions of dealing with the highly charged system? Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 09:58:36 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks Justin. I tried your suggestions by either increase more windows and change the force constant, but it seems the samplings are still bad in some windows. When I did pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got different configurations at certain reaction coordinates. And the windowed umbrella sampling seems depends strongly on the initial configurations in that window. Therefore I got different PMFs using pulling in (0 0 1) direction and reverse pulling in （0 0 -1) direction. How long are each of the simulations in each window? Sufficient sampling should eliminate any configurational bias and/or hysteresis. Also, if the pulling that sets up the initial configurations is done slowly enough, you won't see these problems. Sounds to me like you're pulling too fast or hard, such that the system is not stable. In my simulation, I exert constraints on phosphate atoms in z direction, so there is no lipid flip-flop and the membrane will be stable at high temperatures. Then I am thinking of increasing temperature in those bad windows to enhance sampling... I don't know if I can make a convincing argument here, but intuitively, these windows would be sampling in a different ensemble, so the free energy landscape in these windows would be discontinuous with any adjacent windows that are done at different temperatures, and perhaps the forces required to restrain your peptide at a given COM distance will still result in a discontinuous PMF. I would also suspect that g_wham can't handle this situation; it has a -temp flag, but it only takes one value. So if you construct your PMF curve using WHAM, but supply incorrect or inconsistent information, I certainly wouldn't believe the result. I guess the main point is, there are tons of published demonstrations of peptides and other molecules crossing a membrane with SMD and umbrella sampling, so it should be possible to generate stable configurations without any funny tricks. -Justin best regards, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, 22 February 2011 09:35:37 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows? If
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Jianguo Li wrote: Thanks for your comments, Justin. Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time. The pulling rate is 0.001 nm/ps. Is it too fast? Let me clarify things, since I'm not convinced I understand your procedure. You generate a series of configurations with 0.001 nm/ps pulling, but then how many windows do you generate for independent simulations? What are your .mdp parameters during those windows? The pull rate should be 0 during the actual umbrella sampling, to restrain the peptide within the window. What force constant(s) do you use? My system is a little different. My peptide is highly positively charged. The NMR experiments show that the conformation of the peptide in water is very dynamic, so I make it flexible without fixing any secondary structure in Martini model. As was discussed in the last few days, do not interpret changes in structure too directly when using MARTINI. It is not designed to faithfully mimic secondary structure changes. In the membrane, 25% of the lipids are negatively charged, so there are very strong electrostatic attraction between peptides and membrane. During the peptide approaching the membrane from the top, peptide can take different configurations at different reaction coordinates. When pulling the peptide into the membrane, the peptide takes relatively compact structure and interacts with only the top leaflet until the distance becomes smaller than 0.45 nm, after that the peptide becomes extended structure and interacts with both leaflets. This extended structure remains until the distance becomes -1.05 nm. Further pulling leads to compact structure and interacts only with the lower leaflet. So the comformation of the peptide is not symmetric between the center of the bilayer, which leads to Hysteresis. It seems that there is a huge I guess I'm confused here, too. The peptide is compact when interacting with the top leaflet, extended further in the membrane, then compact again when interacting with the lower leaflet. What's strange about that? energy barrier for the peptide to translocate across the membrane because if the initial conformation in a certain window is extended (interacting with both leaflets), then it remains extended. Similarly, it the initial conformation in a certain window is compact (interacting with only one leaflet), it will remain compact. I don't see how that is necessarily unexpected or problematic. Peptides will change conformation depending on their environment. If you want a static structure to cross the membrane (which may or may not represent reality) you'll have to introduce some kind of intramolecular restraints. -Justin Any Suggestions of dealing with the highly charged system? Cheers, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Tuesday, 22 February 2011 09:58:36 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks Justin. I tried your suggestions by either increase more windows and change the force constant, but it seems the samplings are still bad in some windows. When I did pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got different configurations at certain reaction coordinates. And the windowed umbrella sampling seems depends strongly on the initial configurations in that window. Therefore I got different PMFs using pulling in (0 0 1) direction and reverse pulling in （0 0 -1) direction. How long are each of the simulations in each window? Sufficient sampling should eliminate any configurational bias and/or hysteresis. Also, if the pulling that sets up the initial configurations is done slowly enough, you won't see these problems. Sounds to me like you're pulling too fast or hard, such that the system is not stable. In my simulation, I exert constraints on phosphate atoms in z direction, so there is no lipid flip-flop and the membrane will be stable at high temperatures. Then I am thinking of increasing temperature in those bad windows to enhance sampling... I don't know if I can make a convincing argument here, but intuitively, these windows would be sampling in a different ensemble, so the free energy landscape in these windows would be discontinuous with any adjacent windows that are done at different temperatures, and perhaps the forces required to restrain your peptide at a given COM distance will still result in a discontinuous PMF. I would also suspect that g_wham can't handle this situation; it has a -temp flag, but it only takes one value. So if you construct your PMF curve using WHAM, but supply incorrect or inconsistent information, I certainly wouldn't believe the result. I guess the main point is, there are tons of published
[gmx-users] Can g_wham support using different temperature for different windows?
Sounds like unconverged sampling. You would be astounded how long systems like this can take to converge. An all-atom simulation like this can easily require 10 us (microseconds!) per umbrella. I don't know about martini, probably a lot less. Chris. -- original message -- Thanks Justin. I tried your suggestions by either increase more windows and change the force constant, but it seems the samplings are still bad in some windows. When I did pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got different configurations at certain reaction coordinates. And the windowed umbrella sampling seems depends strongly on the initial configurations in that window. Therefore I got different PMFs using pulling in (0 0 1) direction and reverse pulling in ?0 0 -1) direction. In my simulation, I exert constraints on phosphate atoms in z direction, so there is no lipid flip-flop and the membrane will be stable at high temperatures. Then I am thinking of increasing temperature in those bad windows to enhance sampling... best regards, Jianguo -- 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] membrane bilayer simulation by OPLS FF
Dear All: I am using OPLS force field (OPLS FF) to do molecular dynamics simulations. My system contains DPPC lipid, protein and a small molecule. I have the following questions: 1, where can I get the topology files for the DPPC lipids? 2, How to prepare the topology files for the small molecules? I plan to calculate the charges of each atoms by QM method.After I got the charges and atom radius, how to prepare the topology files? 3, I am using GROMACS 3 and I found there are three all-atom force fields there: -- 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges - among them, 6, 7, and 8 are all-atom force fields, right? My question is are 7 and 8 also OPLS force fields? If so, which one is recommendated to use in lipid-protein complex systems MD simulations? What are the differences between 6, 7 and 8. Sincerely Yours Ruo-Xu Gu -- 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] %exist hydrogen bond
Dear Justin
My simulation system contains protein, dna and water.
I used your script already for obtaining %exist hydrogen bonds between
protein and dna:
#!/usr/bin/perl
#
# plot_hbmap.pl - plot the probability of finding a particular hydrogen bond
# based on several input files:
# 1. coordinate file (for atom naming) - MUST be a .pdb file with NO CHAIN
#IDENTIFIERS
# 2. hbmap.xpm
# 3. hbond.ndx (modified to contain only the atom numbers in the [hbonds...]
#section, nothing else)
#
use strict;
unless(@ARGV) {
die Usage: perl $0 -s structure.pdb -map hbmap.xpm -index hbond.ndx\n;
.
.
.
.
It worked good and output file (summary_Hbmap.dat) was as follows:
#DonorAcceptor % Exist.
0.000
NGL1 NDT64 O4 1.195
NGL1 NDT82 O4 0.797
ARG57 NH2DA79 O1P 19.920
ARG57 NH2DA80 O1P 0.797
ARG57 NH2DA80 O2P 16.335
ARG57 NH1DA80 O2P 43.426
Now I want to use your script for obtaining %exist hydrogen bonds
between protein and water molecules, but output file
(summary_Hbmap.dat) is as follows:
#DonorAcceptor % Exist.
NGL1 N 0.160
ARG58 NH2 0.400
ARG58 NH2 43.565
ARG58 NH1 1.839
ARG58 NH1 0.080
ARG58 NH1 21.663
What is problem?
Please guide me about that.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
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] membrane bilayer simulation by OPLS FF
7 and 8 have nothing to do with OPLS-AA. As the text tells you, it is the Encad forcefield (http://www.sklogwiki.org/SklogWiki/index.php/ENCAD_%28force_field%29) So that then leaves you with the OPLS-AA for you to use :-) Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of mirc...@sjtu.edu.cn Sent: Tuesday, 22 February 2011 4:18 PM To: gmx-users@gromacs.org Subject: [gmx-users] membrane bilayer simulation by OPLS FF Dear All: I am using OPLS force field (OPLS FF) to do molecular dynamics simulations. My system contains DPPC lipid, protein and a small molecule. I have the following questions: 1, where can I get the topology files for the DPPC lipids? 2, How to prepare the topology files for the small molecules? I plan to calculate the charges of each atoms by QM method.After I got the charges and atom radius, how to prepare the topology files? 3, I am using GROMACS 3 and I found there are three all-atom force fields there: -- 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges - among them, 6, 7, and 8 are all-atom force fields, right? My question is are 7 and 8 also OPLS force fields? If so, which one is recommendated to use in lipid-protein complex systems MD simulations? What are the differences between 6, 7 and 8. Sincerely Yours Ruo-Xu Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] diffusion coefficients
Hello, I'm investigating the diffusion coefficient of gases in liquids. Therefore, I insert some molecules with the genbox tool in an equilibrated system. After a NPT run to adjust the density, I'm running an NVT simulation to calculate the diffusion coefficient (g_msd). MSD of the liquids are quite linear, but the gas MSDs show sometime fluctuations, even with negative slopes within the run. What can be the problem or is this strategy right? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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] Can g_wham support using different temperature for different windows?
Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electrostatic attraction between peptide and membrane. To get the PMF, I did the following: (1) I did pulling simulation along (0 0 -1) direction to pull my peptide across the membrane. Then I got different configurations corresponding to different windows along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6d0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force constant in these windows. From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we can classify the peptide conformation to be either extended (interacting with two bilayers) or compact (interacting with only one bilayer). Ideally, the peptide conformation should be similar for d=x and d=-x. The problem is that the configuration of peptide is not symmetric with respect to the bilayer center. For example, the peptide configuration is compact at d=0.6 and d=0.9, but the peptide is extended at d=-0.6 and d=-0.9. This leads Hysteresis. If I use g_wham to generate PMF, then the PMF is not symmetric with respect to the bilayer center. Using more number of windows and different force constant did not remove the problem. In my opinion, at least in some windows, the peptide should sample both compact and extended structure. But what I found is that the windowed umbrella simulation depends on the initial peptide conformation. If the initial peptide conformation is compact, then after 100 ns, it is still compact; if the initial peptide in that window is extended, the final configuration is also extended. I also tried to run longer equilibrium time (e.g., 200 ns), but the problem still exists. My question is how to increase sampling of the peptide conformation? I just think of two choices: (1) use high temperature (e.g., 500K) at those bad windows. As I mentioned, I am wondering if g_wham can unbias the effect of using different temperatures in different windows. (2) use REMD in those bad windows. These need a lot of computational resources. Is there any other method to deal with the insufficient sampling? Any suggestions are welcome, thanks for your time reading this email! Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 11:13:05 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks for your comments, Justin. Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time. The pulling rate is 0.001 nm/ps. Is it too fast? Let me clarify things, since I'm not convinced I understand your procedure. You generate a series of configurations with 0.001 nm/ps pulling, but then how many windows do you generate for independent simulations? What are your .mdp parameters during those windows? The pull rate should be 0 during the actual umbrella sampling, to restrain the peptide within the window. What force constant(s) do you use? My system is a little different. My peptide is highly positively charged. The NMR experiments show that the conformation of the peptide in water is very dynamic, so I make it flexible without fixing any secondary structure in Martini model. As was discussed in the last few days, do not interpret changes in structure too directly when using MARTINI. It is not designed to faithfully mimic secondary structure changes. In the membrane, 25% of the lipids are negatively charged, so there are very strong electrostatic attraction between peptides and membrane. During the peptide approaching the membrane from the top, peptide can take different configurations at different reaction coordinates. When pulling the peptide into the membrane, the peptide takes relatively compact structure and interacts with only the top leaflet until the distance becomes smaller than 0.45 nm, after that the peptide becomes extended structure and interacts with both leaflets. This extended structure remains until the distance becomes -1.05 nm. Further pulling leads to compact structure and interacts only with the lower leaflet. So the comformation of the peptide is not symmetric between the center of the bilayer, which leads to Hysteresis. It seems
