[gmx-users] RMS deviation after position restraint dynamics
Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? Thank You, Regards, Sukesh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RMS deviation after position restraint dynamics
sukesh chandra gain wrote: Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? You should read in the manual about how position restraints are implemented. If you wanted zero RMS deviation in one of your observables, perhaps you should re-think why you are running *dynamics*. :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RMS deviation after position restraint dynamics
A restraint is not a constraint, and assuming that you are simulating your system at a finite temperature, you should expect to see some fluctuations in a given atom's position. Josh On May 17, 2009, at 11:47 PM, sukesh chandra gain wrote: Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? Thank You, Regards, Sukesh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://nature.berkeley.edu/~jadelman Berkeley, CA 94720 USA jadel...@berkeley.edu -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How can i know if the protein swell during the MD simulation?
Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess these. Not the simplest thing... Cheers, Tsjerk On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the manual about available analysis tools. -Justin Thank you Lin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rdf -xy
Dear gmx-users, I simulate a vapor/water/decane/vapor interface system. The interface is xy plane. I want to analysis water structure at the interface using g_rdf program along z axis with -xy parameter. But the calculation is hanged as the following: Select a reference group and 1 group Group 0 ( OW) has 2508 elements Group 1 ( HW*) has 5016 elements Select a group: 0 Selected 0: 'OW' Select a group: 0 Selected 0: 'OW' trn version: GMX_trn_file (single precision) Skipping frame 3000 time 4100.000 I used the following the operation g_rdf -f -s -n -bin 100 -xy -o Is the runing normal? Please give me some suggestion. Thanks a lot! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How can i know if the protein swell during the MD simulation?
How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess these. Not the simplest thing... Cheers, Tsjerk On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the manual about available analysis tools. -Justin Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How can i know if the protein swell during the MD simulation?
stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu bhanui...@gmail.com wrote: How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess these. Not the simplest thing... Cheers, Tsjerk On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to see the swollen protein? How do you define the term swelling? This again sounds like another issue on defining your own criteria for the expected behavior and reading the manual about available analysis tools. -Justin Thank you Lin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Constraints specified in .mdp as well as in .top files
Hi, I think the manual is pretty clear on this: constraints: none No constraints except for those defined explicitly in the topology, i.e. bonds are represented by a harmonic (or other) potential or a Morse potential (depending on the setting of morse) and angles by a harmonic (or other) potential. Berk Date: Sat, 16 May 2009 12:04:09 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Constraints specified in .mdp as well as in .top files Vishwanath Dalvi wrote: Thank you for your response. I am still unclear as to how the whole thing works (and the manual is no help). If I do specify (in the .mdp file) something like constraints = all-bonds, will that override the harmonic-bond interactions specified in the .itp files? Don't know. Check the manual, or try it and see. Either your .log file output or inspection of gmxdump of your .tpr might be useful here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_rdf -xy
Hi, g_rdf -xy does not do what you want. It determines rdf's using only the x and y components of the distance and averages over z. g_rdf hangs probably because you use -nbin 100, which sets bins with a width of 100 nm (and not 100 bins as you probably thought). There is currently no Gromacs tools which can easily do what you want. Berk Date: Mon, 18 May 2009 16:12:16 +0800 From: hyx...@mail.ipc.ac.cn To: gmx-users@gromacs.org Subject: [gmx-users] g_rdf -xy Dear gmx-users, I simulate a vapor/water/decane/vapor interface system. The interface is xy plane. I want to analysis water structure at the interface using g_rdf program along z axis with -xy parameter. But the calculation is hanged as the following: Select a reference group and 1 group Group 0 ( OW) has 2508 elements Group 1 ( HW*) has 5016 elements Select a group: 0 Selected 0: 'OW' Select a group: 0 Selected 0: 'OW' trn version: GMX_trn_file (single precision) Skipping frame 3000 time 4100.000 I used the following the operation g_rdf -f -s -n -bin 100 -xy -o Is the runing normal? Please give me some suggestion. Thanks a lot! H.Y. Xiao _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp
Protonate does the job of adding all of the hydrogens but non-polar hydrogens are not recognised by pdb2gmx so that the topology file isn't created. Apparently grompp needs the *.top file in input (It says Input/Output error upon giving only the *.gro file in input). Does this mean that I can't run an MD simulation with a molecule with non-polar hydrogens. Thank you for your help, Stefano Justin A. Lemkul ha scritto: Stefano Meliga wrote: Hello, I would like to add non-polar hydrogens as well as the polar ones. Does anybody know if that is possible? I haven't found any related option of the function pdb2gmx. protonate -h -Justin Thanks, Stefano. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rdf -xy
Dear Berk, I am sorry that I have a mistake in the first letter. In fact I used -bin 0.05, not 100. Yet the result is hanged. Maybe as you said, the current Gromacs can not realize what I want to do. Thanks again! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Input/Output error using grompp
Hello, I can't get rid of an error occurring using grommp: --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: grompp.mdp --- my command line is: grompp -r 4AKEpolHsol.gro -4AKEpolH.top -o 4AKEpolH.tpr -po 4AKEpolH.mdp I am not giving any mdp file in input because I didn't run an simulation yet. I want the preprocessed files .tpr and .mdp in output. Can it be an issue related with my cpp pre-processor? Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Input/Output error using grompp
Stefano Meliga wrote: Hello, I can't get rid of an error occurring using grommp: --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: grompp.mdp --- my command line is: grompp -r 4AKEpolHsol.gro -4AKEpolH.top -o 4AKEpolH.tpr -po 4AKEpolH.mdp I am not giving any mdp file in input because I didn't run an simulation yet. I want the preprocessed files .tpr and .mdp in output. Can it be an issue related with my cpp pre-processor? you have to provide this file. you could try touch grompp.mdp which will generate a default mdout.mdp file which you can modify. Thanks, Stefano ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file for local pressure
Dear sir, I am calculating local pressure by gromacs-localp. My .mdp file is following integrator = sd ; stochastic dynamics - Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps = 5 ; total 500/5=100 ps nstcomm = 1 ; freq. for cm-motion removal tinit= 0 ; starting time (ps) constraints = all-bonds ; constraint for all bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default nstxout = 1000; T(x_out) 10 ps nstvout = 1000; T(v_out) 10 ps nstfout = 0 ; T(f_out) nstlog = 250 ; energies to log (0.5 ps) nstenergy= 250 ; energies to energy file ns_type = grid; nl type nstlist = 10 ; Freq. to update neighbour list rlist= 1.0 ; nm (cutoff for short-range nl) ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy coulombtype = PME ;Reaction-Field ; Coulomb interactions rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!) epsilon_r= 80.0; dielectric constant for reaction field vdwtype = Cut-off ; Wan der Waals interactions rvdw = 1.0 ; nm (LJ cut-off) optimize_fft = yes ; Temperature coupling Tcoupl = no ; no effect when integrator = sd tc-grps = POPC SM CHOL SOL tau_t= 0.1 0.1 0.1 0.1 ref_t= 296 296 296 296 ; Pressure coupling ;Pcoupl = no Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 1.01.0 ; ps compressibility = 4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K) ref_p= 1.01.0 ; bar ; Generate velocites in the beginning gen_vel = yes gen_temp = 296.0 gen_seed = 173529 ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 It gives following error --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: readir.c, line: 454 Fatal error: Expected 2 elements for wall_atomtype, found 0 --- Could you please tell me where my fault is? Thanks a lot in advance. Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Input/Output error using grompp
Am 18.05.2009 um 13:26 schrieb Stefano Meliga: my command line is: grompp -r 4AKEpolHsol.gro -4AKEpolH.top -o 4AKEpolH.tpr -po 4AKEpolH.mdp what's your 2nd argument? the grompp.mdp is afaik mandatory - you can just create an empty one before, e.g. if you grompp for genion... touch dummy.mdp grompp -f dummy.mdp genion... Can it be an issue related with my cpp pre-processor? Gromacs 4 has it's own built in pre-processor from what I know. Best Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp
Stefano Meliga wrote: Protonate does the job of adding all of the hydrogens but non-polar hydrogens are not recognised by pdb2gmx so that the topology file isn't created. Apparently grompp needs the *.top file in input (It says Input/Output error upon giving only the *.gro file in input). Does this mean that I can't run an MD simulation with a molecule with non-polar hydrogens. Choose an all-atom force field with pdb2gmx (i.e., OPLS-AA). The hydrogens will be added by pdb2gmx. -Justin Thank you for your help, Stefano Justin A. Lemkul ha scritto: Stefano Meliga wrote: Hello, I would like to add non-polar hydrogens as well as the polar ones. Does anybody know if that is possible? I haven't found any related option of the function pdb2gmx. protonate -h -Justin Thanks, Stefano. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp
Stefano Meliga wrote: Protonate does the job of adding all of the hydrogens but non-polar hydrogens are not recognised by pdb2gmx so that the topology file isn't created. Thus you've discovered that pdb2gmx isn't magic. It can only create topologies whose building blocks are already defined in the so-called residue topology files (.rtp extensions). You may need to create entries for these. Search the wiki and chapter 5 of the manual. Depending on your need, you may be better off using some alternative topology-generating software. Apparently grompp needs the *.top file in input (It says Input/Output error upon giving only the *.gro file in input). grompp pre-processes a topology (.top file) in the context of a set of simulation parameters (.mdp file) and a given starting configuration (.gro file) to produce a run input file (.tpr). All these three input elements are necessary; others are optional. Does this mean that I can't run an MD simulation with a molecule with non-polar hydrogens. You can run one, but you need to generate a .top file first. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?
Dear GROMACS Masters, is there a trick to obtain coordinates and velocities of center of mass of each water molecule? Have a look at g_traj, although to analyze each molecule separately could take many iterations with specific index groups. g_traj can really do it (for coordinates), thanks! g_traj with -mol option was what I needed. It is documented in the third sentence of the DESCRIPTION section of g_traj manual... When -mol is set, the numbers in the index file are interpreted as molecule numbers and the same procedure as with -com is used for each molecule. -Bohumir ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: parameter of RB potential for OPLS force field
Dear Justin: Thanks for your response. I saw this in the ffoplsaabon.itp, which I think is a Periodic potential. [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations SI OS1 0.000 3.766 3 SI OH1 0.000 3.766 3 Does this mean that we can still use a periodic potential combined with OPLS force field since it seems OPLS also consists of the periodic potential besides RB. It doesn't have to be necessary to use RB for the proper dihedral when you use OPLS force field, right? Thank you so much for your help! On Fri, May 15, 2009 at 6:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: There is a periodic dihedral within ffoplsaabon.itp which points to a reference. Perhaps these are the parameters you are referring to. If not, check out the bottom of ffoplsaabon.itp and read that paper to see if the parameters will suit your needs. If you need an R-B dihedral, you may have to parameterize it yourself; not an easy task. -Justin Yanmei Song wrote: They are CH3-SI-O-SI, SI-O-SI-CH3 and SI-O-SI-O. I have looked up ffoplsaabon.itp. it doesn't include any dihedral consisting of SI. And the literatures only have the parameters for periodic potential. Thank you so much for your kind help! On Fri, May 15, 2009 at 4:00 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Yes, I have read that part and still have no idea how can I do that. That part tells us how to transfer from the OPLS parameters Vi to RB potential in GROMOS force field Ci. Now what I have is phi and k for periodic potential. Is there any way I can get Ci for RB potential from phi and k in order to use OPLS force field? I don't know if there is a direct conversion. There are, however, over 1000 existing dihedrals in ffoplsaabon.itp; which dihedral are you looking for that you can't find? -Justin On Fri, May 15, 2009 at 3:34 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Please keep all Gromacs-related correspondence on the gmx-users list. That way, the discussion is archived for the later benefit of others, and you have a chance to reach a wider audience of individuals who may be able to help you. That said, read the manual, section 4.2.12. -Justin Yanmei Song wrote: Dear Justin: If I have the parameters of GROMOS force field for the proper dihedral, which i think they are phi and k for function 1 for periodic type. I wanted to use OPLS force field. As far as I know in OPLS the dihedral was RB potential in fuction 3. So my question is do you know any method I can transfer this parameter to RB parameters? Or these two potentials have no connections? Thanks --Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
[gmx-users] how to add shear force in gromacs
Hi all users, I just wonder how I can add the shear force in gromacs. I have checked the manual but failed to find some effective ways to do that. Any suggestions will be highly appreciated. Thank you very much. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] shift function for vdwtype and density
Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: parameter of RB potential for OPLS force field
Yanmei Song wrote: Dear Justin: Thanks for your response. I saw this in the ffoplsaabon.itp, which I think is a Periodic potential. So check out table 5.4 in the manual and find out for sure! [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations SI OS1 0.000 3.766 3 SI OH1 0.000 3.766 3 Does this mean that we can still use a periodic potential combined with OPLS force field since it seems OPLS also consists of the periodic potential besides RB. It doesn't have to be necessary to use RB for the proper dihedral when you use OPLS force field, right? What's necessary is to use parameters and functional forms that have been demonstrated to be parameterized for your observables. Mixing functional forms doesn't seem like something to encourage, but if it's been done already and you're happy with their results, then go for it. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shift function for vdwtype and density
Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shift function for vdwtype and density
Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shift function for vdwtype and density
Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Molecule Jumps
Hi All, I just wanted to let you know how I resolved my problem, in case anyone else experiences a similar problem in the future. My structure spanned all four quadrants around the origin (i.e. the 4 vertices of my structure were (-x, -y), (-x,y), (x,-y), (x,y)). I think because it spanned all 4 quandrants, this caused the molecule to jump from corner to corner within the box. Once I translated my molecule such that its coordinates were entirely within the positive x,y quandrant, the molecule no longer jumped around in the box. Best regards, Darrell Koskinen Date: Sun, 17 May 2009 20:08:06 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Molecule Jumps To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a0fe206.4000...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi All, I have an array of molecules above a grapehene sheet in my simulation. However, when I look at my trajectory file (.trr) in VMD the array of molecules is split into 4 sections with each section located at what looks to be the corners of the simulation box. And the graphene sheet does not stay stationary as it should, but rather jumps from corner to corner. I tried to resolve this problem by running the following command: trjconv -f traj.trr -o trajout.trr -center -pbc nojump However, this did not resolve the problem. Is there something else I need to do to resolve this problem? No, some combination of options to trjconv should work. Sometimes two two separate invocations with separate options are needed. BTW ...does not stay stationary as it should is not true... you're wanting a certain feature for your visualization convenience, and during the simulation GROMACS hadn't permitted you to choose which of the infinite equivalent possibilities it should present in the trajectory. You're choosing that now, *after* the fact. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shift function for vdwtype and density
Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shift function for vdwtype and density
Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] shift function for vdwtype and density
Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php --Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS
Re: [gmx-users] shift function for vdwtype and density
Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read. -Justin On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was parameterized. The greater the extent to which your .mdp conditions differ from those conditions, the greater the likelihood that the parameterization is no longer valid. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] shift function for vdwtype and density
Perhaps I can contribute something else that might be a bit more useful. It just occurred to me that if you are only changing the vdwtype parameter, then you are not correctly implementing the shift function. See here for proper use of a shift potential: http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw Take note of the necessary changes to vdw_shift, and potentially rlist. A few quick tests of the shift function indicate the following: Case 1. Plain cutoff's at 1.2 nm Density: 988 kg/m^3 Case 2. Shift potential (no other changes, i.e. rvdw_switch = 0, rvdw = 1.2) Density: 962 kg/m^3 Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2) Density: 983 kg/m^3 -Justin Justin A. Lemkul wrote: Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read. -Justin On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? Maybe not. Check out the paper in which TIP5P was
RE: [gmx-users] mdp file for local pressure
The error message explicitly tells you what is wrong: Expected 2 elements for wall_atomtype, found 0 And looking in your .mdp file ... ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 On the wall_atomtype line, you have defined zero elements and you should have two. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Molecule Jumps
darre...@ece.ubc.ca wrote: Hi All, I just wanted to let you know how I resolved my problem, in case anyone else experiences a similar problem in the future. My structure spanned all four quadrants around the origin (i.e. the 4 vertices of my structure were (-x, -y), (-x,y), (x,-y), (x,y)). I think because it spanned all 4 quandrants, this caused the molecule to jump from corner to corner within the box. Once I translated my molecule such that its coordinates were entirely within the positive x,y quandrant, the molecule no longer jumped around in the box. ...only because the critical feature of the molecule (COM? first atom?) didn't drift outside the box in which you placed it. I don't know (or care) what the conventions of GROMACS or your visualization program are, but the general solution is to forget about it until you go to visualize your trajectory, and then fiddle with trjconv until you're happy with the result. :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] shift function for vdwtype and density
Dear Justin: Thanks so much for your effort and information. Perhaps I did not set the proper value for vdw_switch. I will try some value. I really appreciate your nice help! On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: Perhaps I can contribute something else that might be a bit more useful. It just occurred to me that if you are only changing the vdwtype parameter, then you are not correctly implementing the shift function. See here for proper use of a shift potential: http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw Take note of the necessary changes to vdw_shift, and potentially rlist. A few quick tests of the shift function indicate the following: Case 1. Plain cutoff's at 1.2 nm Density: 988 kg/m^3 Case 2. Shift potential (no other changes, i.e. rvdw_switch = 0, rvdw = 1.2) Density: 962 kg/m^3 Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2) Density: 983 kg/m^3 -Justin Justin A. Lemkul wrote: Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read. -Justin On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For
Re: [gmx-users] shift function for vdwtype and density
Justin A. Lemkul wrote: Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much! No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read. Actually this is not so easy. Jorgensen has never published the way he treats cut-offs, but he was friendly enough to let me know, so we have actually done it: David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006) If you look in the appendix you can find the one and only shifting method for OPLS. However This is not to be recommended since the effect is very different for MD and MC (what Jorgensen uses). In MD the official method will give horrible artifacts. In other words, you have to use something better. Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations. -Justin On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I did the bulk water and bulk polymer system, I found the densities change with different cutoff and vdwtype conditions. Is this a artifact? Or the larger cutoff, the more accurate result we can get? Every parameter you specify will affect the results you see. I agree with Mark - look up the original reference for TIP5P and see what parameters are recommended. Also read the subsequent literature that has used TIP5P to see what modifications (electrostatic treatment, vdW treatment, etc) are appropriate or even more accurate. Also realize that using vdwtype = shift may not be the best solution. I only suggested as a guess for something to try back when you were getting bizarre results with your polymer. Have you ever tried dispersion correction when using vdwtype = cutoff? I routinely use such a setup and have never seen any really bizarre behavior. -Justin On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982. Thanks! So your system is water + polymer? In that case, you have an added variable - the interaction between the water and your polymer. What you should probably be more concerned with the what the bulk density of the whole system is. I have found that analyzing densities of portions of mixed systems does not give an accurate result. -Justin On Mon, May 18, 2009 at 3:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift
