[gmx-users] ligand-protein simulation
Dear all gromacs users, I have run a protein-ligand simulations. However, the position of the ligand is not reasonable after 10ns simulation. There is no problem with the force field paramers of the ligand. I am trying to constrict the ligand move for 500ps simulation. But i do not know whether it will work. Any good idea is appreciated :) Best wishes Fugui-- 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] Lysozyme in Water at different pH and Ionic strength
It is impossible. But you can add proton to the acidic amino acid. At 2013-11-01 20:36:41,Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? 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 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:Re: [gmx-users] ligand-protein simulation
Hi Justin, Thank you very much for your response. I used GAFF force field parameters for the ligand. I have done another short MD simulation, and this time everything seems fine, so i have no idea where the problem is from. Best wishes Fugui At 2013-11-01 20:41:46,Justin Lemkul jalem...@vt.edu wrote: On 11/1/13 5:37 AM, xiao wrote: Dear all gromacs users, I have run a protein-ligand simulations. However, the position of the ligand is not reasonable after 10ns simulation. There is no problem with the force field paramers of the ligand. I am trying to constrict the ligand move for 500ps simulation. But i do not know whether it will work. Any good idea is appreciated :) Usually when something misbehaves, the topology is the first likely source of error. How have you concluded that it is suitable? Since we don't know what you're doing (description of your protocol, or even better, .mdp files), it could simply be that you're doing something that causes the physical model to be wrong. Provide that information and you're more likely to get a quick and productive response. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] problem with the amb2gmx.pl
Dear all, I am doing membrane protein simulation by using amber force field. The lipid force field parameters are from the lipid11.dat from Amber. Firstly, i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top and xx.gro files. However, i found there is some problem with the xx.top files. For example, there are two dihedral parameters, and they should be same, but in the xx.top file (gromacs form) ,they are different. I have no idea where the problem is from. Any information is appreciated! Fugui -- 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:Re: [gmx-users] problem with the amb2gmx.pl
Hi Alan, Thank you very much! The problem is solved. The reason is that amb2gmx cannot distinguish the proper and improper dihedrals. Best wishes Fugui At 2013-10-09 21:58:29,Alan alanwil...@gmail.com wrote: Hi, try ACPYPE. Alan On 9 October 2013 14:07, xiao helitr...@126.com wrote: Dear all, I am doing membrane protein simulation by using amber force field. The lipid force field parameters are from the lipid11.dat from Amber. Firstly, i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top and xx.gro files. However, i found there is some problem with the xx.top files. For example, there are two dihedral parameters, and they should be same, but in the xx.top file (gromacs form) ,they are different. I have no idea where the problem is from. Any information is appreciated! Fugui -- 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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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] control atom in .hdb file
Dear all, I am developing the force field paramters of an organic molecule. I have a trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how to write to control atom. The manual said that: Three or four control atoms (i,j,k,l), where the first always is the atom to which the H atoms are connected. The other two or three depend on the code selected. I can know the meaning of the first control atom, but i am confused by The other two or three depend on the code selected. I think the other two control atoms are the heavy atoms that are the neighbor of the heavy atom that is needed to add hydrogen. But how to define the control atoms for the -CH3 group, because there is only one heavy atom that is connected to the -CH3 group? Any suggestion is appreciated. Best wishes Fugui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.
Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using MM method and the QM method. Firstly, i plan to scan the bond of interest up to 0.1 angstrom from the equilibrium value at a step size of 0.005 angstrom while optimizing the structure at each step by using QM method. Secondly, i calculate the potential energy of each structure obtained in the previous QM optimizaiton step. Thirdly, i will calculate the energy difference between QM and MM calculation, and finally fit the force constant of the bond using the energy difference between QM and MM energy. My question is that how i calculate the potential energy of each structure obtained in QM step? I think i can get an potential energy in energy minization step by using grompp method, but i am not sure whethe r it is the energy i needed. Any advice is appreciated. Best wishes Fugui -- 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:Re: [gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.
Dear Justin, Thank you so much for your help! Best wishes Fugui At 2013-07-28 03:52:47,Justin Lemkul jalem...@vt.edu wrote: On 7/27/13 11:48 AM, xiao wrote: Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using MM method and the QM method. Firstly, i plan to scan the bond of interest up to 0.1 angstrom from the equilibrium value at a step size of 0.005 angstrom while optimizing the structure at each step by using QM method. Secondly, i calculate the potential energy of each structure obtained in the previous QM optimizaiton step. Thirdly, i will calculate the energy difference between QM and MM calculation, and finally fit the force constant of the bond using the energy difference between QM and MM energy. My question is that how i calculate the potential energy of each structure obtained in QM step? I think i can get an potential energy in energy minization step by using grompp method, but i am not sure whe ! the r it is the energy i needed. Any advice is appreciated. http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Implicit solvent MD is not fast and not accurate.
Dear Gromacs users: I did a protein MD using implicit solvent and Amber 99SB force filed. However, i found that the implicit solvent is not faster than explicit solvent, and what is worse is that it is also not accurate. The system is a protein-ligand complex. Firstly, i run a minimization, and then i did a production MD. The explicit solvent MD can give nearly same strucuture as the crystal structure after 10ns MD. However, there is a significant change in the ligand after 1ns MD in implicit solvent. My .mdp file is as follows: title = OPLS Lysozyme MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 1000 ; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0 ; short-range electrostatic cutoff (in nm) rvdw = 0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ; Particle Mesh Ewald for long-range vdwtype = cut-off pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau_t = 0.1; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; ; comm-mode = angular comm-grps = system ; ; pcoupl = no ; Pressure coupling on in NPT pbc = no ; 3-D PBC gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; implicit_solvent= GBSA gb_algorithm= OBC ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 Can anyone give me some suggestions? BW Fugui -- 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:Re: [gmx-users] Implicit solvent MD is not fast and not accurate.
Dear Justin, Thank you very much for your reply. I found that the speed of implict MD is slower that explict MD. For examplex, the speed of an explict MD for a protein of 300 amino acids is about 3ns per day, however, the implicit solvent is about 1.5ns per day. With respect to the accuracy of implicit solvent, the result shows bad result. There are two carbon atom types which are not in the gbsa.itp, and i just copied some carbon atom type in gbsa.itp because i find that there is no big difference between the carbon parameters. I do not know whether this is the reason. BW Fugui At 2013-03-27 21:45:42,Justin Lemkul jalem...@vt.edu wrote: On Wed, Mar 27, 2013 at 9:27 AM, xiao helitr...@126.com wrote: Dear Gromacs users: I did a protein MD using implicit solvent and Amber 99SB force filed. However, i found that the implicit solvent is not faster than explicit solvent, and what is worse is that it is also not accurate. The system is a protein-ligand complex. Firstly, i run a minimization, and then i did a production MD. The explicit solvent MD can give nearly same strucuture as the crystal structure after 10ns MD. However, there is a significant change in the ligand after 1ns MD in implicit solvent. My .mdp file is as follows: title = OPLS Lysozyme MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 1000 ; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0 ; short-range electrostatic cutoff (in nm) rvdw = 0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ; Particle Mesh Ewald for long-range vdwtype = cut-off pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau_t = 0.1; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; ; comm-mode = angular comm-grps = system ; ; pcoupl = no ; Pressure coupling on in NPT pbc = no ; 3-D PBC gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; implicit_solvent= GBSA gb_algorithm= OBC ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = -1 Can anyone give me some suggestions? Performance issues are known. There are plans to implement the implicit solvent code for GPU and perhaps allow for better parallelization, but I don't know what the status of all that is. As it stands (and as I have said before on this list and to the developers privately), the implicit code is largely unproductive because the performance is terrible. As for the accuracy assessment, I think you need to provide better evidence of what you mean. A single simulation is not definitive of anything, and moreover, some differences between explicit and implicit are likely given the lack of solvent collisions. The implicit trajectory will probably sample states that are inaccessible (or at least very rare) in the explicit trajectory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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
Re:Re: Re: [gmx-users] Implicit solvent MD is not fast and not accurate.
Dear Justin, Thank you very much for your suggetions. BW Fugui At 2013-03-27 22:15:23,Justin Lemkul jalem...@vt.edu wrote: On Wed, Mar 27, 2013 at 10:11 AM, xiao helitr...@126.com wrote: Dear Justin, Thank you very much for your reply. I found that the speed of implict MD is slower that explict MD. For examplex, the speed of an explict MD for a protein of 300 amino acids is about 3ns per day, however, the implicit solvent is about 1.5ns per day. I know. This is what I mean about the need for improving the capabilities of the code. The main point of the implicit solvent approach is that it should be faster. With respect to the accuracy of implicit solvent, the result shows bad result. There are two carbon atom types which are not in the gbsa.itp, and i just copied some carbon atom type in gbsa.itp because i find that there is no big difference between the carbon parameters. I do not know whether this is the reason. You need to establish whether what you did was appropriate or not before you begin accusing Gromacs of being inaccurate. If you observe inconsistencies, errors, poor energy conservation, etc. in the context of some known system, then that might be worth investigating. Problems with a custom topology are more likely to be due to the topology than to the software using it. GB atom types are one possible source of error, but in parametrization, there are plenty of things that can go wrong before you even get to that point. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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:Re: [gmx-users] problem in converting coarse grained structure to fine strcture
Dear Groetnis, Thank you very much for your nice suggestion. BW Fugui At 2013-03-26 17:34:08,Djurre de Jong-Bruinink djurredej...@yahoo.com wrote: I used the command g_fg2cg to convert a coarse grained structure into corresponding fine strcture, and i found that the water molecues can be transformed correctly, but there is a big mess in the protien , and i could not get correct protein strcture, can anyone give me some suggestion? g_fg2cg only generates an atomistic input structure for the actual reverse transformation run. The atoms are placed at random position within the CG-beads and thus the protein is supposed to be a big mess after this step. Please read http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation; for a more extensive explanation. Groetnis, Djurre -- 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] problem in converting coarse grained structure to fine strcture
Dear gromacs users, I used the command g_fg2cg to convert a coarse grained structure into corresponding fine strcture, and i found that the water molecues can be transformed correctly, but there is a big mess in the protien , and i could not get correct protein strcture, can anyone give me some suggestion? BW Fugui -- 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] helitr...@126.com
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[gmx-users] how to convert Coarse Grained protein structure to all-atom structure
Dear gromacs users: I finished a coarse grained MD of a protein, but i cannot convert the coarse grained structure into all-atom structure, can anybody give me some advice on that? Best wishes Fugui -- 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] the first 10 missing interactions, except for exclusions...
add dihedral parameter for you EPON molecule. Check this: http://oldwww.gromacs.org/pipermail/gmx-users/2005-May/015044.html 2010/10/24 英雄不再寂寞 xiaowu...@qq.com Dear gmxers, I try to simulate a complex system using gmx-4.5.1. I have carried out the minimization without any errors, but when it comes to molecular dynamics, some errors are printed and given below. How to deal with this problem? Please give me some hints. Thanks a lot for any reply. Yours sincerely, Chaofu Wu, Dr. xiaowu...@linux-s38y:~/workshop mdrun -s detamix_md01.tpr -o detamix_md01.trr -c detamix_md01.gro -e detamix_md01.edr -g detamix_md01.log -v -np 4 -N 4 :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.5.1 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, P盲r Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: Option Filename Type Description .. Option Type Value Description -- .. Getting Loaded... Reading file detamix_md01.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Loaded with Money NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Making 1D domain decomposition 4 x 1 x 1 starting mdrun '40 deta + 100 epon862 + 1 SWCNT(10,10)' 400 steps, 4000.0 ps. step 0 NOTE: Turning on dynamic load balancing step 39500, will finish Mon Oct 25 02:51:47 2010vol 0.61 imb F 14% A list of missing interactions: Ryckaert-Bell. of 12880 missing 2 Molecule type 'EPON' the first 10 missing interactions, except for exclusions: Ryckaert-Bell. atoms 11 12 14 16 global 5481 5482 5484 5486 Ryckaert-Bell. atoms 16 21 23 11 global 5486 5491 5493 5481 --- Program mdrun, VERSION 4.5.1 Source code file: domdec_top.c, line: 356 Fatal error: 2 of the 79000 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.5 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Jede der Scherben spiegelt das Licht (Wir sind Helden) xiaowu...@linux-s38y:~/workshop -- 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] Is there anyone who has tip3p.gro?
Hi there, Recently, I cannot add tip3p water in my system, because GMX cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has tip3p.gro, and could you please give me one copy. highly appreciate!! shijun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 65, Issue 122
Thanks for Mark's fast reply, and It really works. Then, I have another qusetion about the manual: It seems that the exclusion just excludes the nonbond potential of LJ interaction, but Buckingham. If we want to turn off all VDW interaction between some atoms, the energy monitor group is a nice choice. I have no idea if I got it right. And, we can't use LJ and Buckingham in a same system. Unfortunately, I met a force-field that most of the nonbond interactions were described by Buckingham, but LJ only for Ow-Ow among water. I chose nbfunct=2 in [defaults] section,and nbfunct=1 in [nonbond_params] for Ow-Ow. As a result, a error message read: *Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR). *I don't know whether it could be settled in gromacs. Sincerely Shijun -- Message: 1 Date: Mon, 21 Sep 2009 06:24:34 + (GMT) From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: who can help me with the force-field? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: fbcb8a00405b.4ab71...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 09/21/09, xiao shijun xshi...@gmail.com wrote: Mark wrote: xiao shijun wrote: Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! Usually you would not define a nonbonded interaction for atoms that are so close together, since their interaction should be able to be modelled adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, an interaction harmonic the O-O distance as a Urey-Bradley term). Thanks for Mark's suggestion. But I want to reproduce the simulation from the other paper, The paper describe the force-field that O-O nonbonded interaction in the same carbonate should be considered. In addition to that, I can't use buckingham potential in [pairs], even choose funct = 2. I am wondering if I want to describe 1-4 interaction by Buckingham, what could I do? This is one application for setting nrexcl for moleculetypes. You don't want exclusions for particles 2 bonds apart, so set this to one. See chapter 5. If that doesn't work, then if the bonded interactions are merely harmonic distance potentials, then GROMACS permits a form of them that doesn't create a bond (bond type 6, IIRC, check chapter 5; or constraint type 2). Thus, the automated exclusion mechanism won't be involved, and you can have Buckingham O-O so long as you have Buckingham for all other LJ interactions. You will need manual exclusions for C-O pairs, I guess. Thus [ atomtypes ] C #nonbonded parameters go here O #nonbonded parameters go here [moleculetype] carbonate [atoms] C O1 O2 O3 [bonds] C-O1 # type 6 C-O2 # type 6 C-O3 # type 6 [exclusions] 1 2 1 3 1 4 Whether this works may depend on whatever else is in your system, though. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] who can help me with the force-field?
Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: who can help me with the force-field?
Mark wrote: xiao shijun wrote: Hi everyone, Recently, I met a problem on the force-field. I am doing something on the calcium carbonate, and want to simulation it with gromacs. The shell model for oxygen has been emploied in my system. When I considered the non-boned potential associated with interactions between atoms in the same CO3 group, I only need to take O-O buckingham interaction into account, but any electric interaction. How could I realize that in my .top file. First, I tried to use [pairs] to eliminate electric interaction, but I can't add the buckingham interaction of O-O because there is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! Usually you would not define a nonbonded interaction for atoms that are so close together, since their interaction should be able to be modelled adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM, an interaction harmonic the O-O distance as a Urey-Bradley term). Thanks for Mark's suggestion. But I want to reproduce the simulation from the other paper, The paper describe the force-field that O-O nonbonded interaction in the same carbonate should be considered. In addition to that, I can't use buckingham potential in [pairs], even choose funct = 2. I am wondering if I want to describe 1-4 interaction by Buckingham, what could I do? BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] What can I to do with the problem: lincs warning and water can not be settled?
hi, The simulation was OK. But when I changed the epsilon of some atoms to get rid of LJ, lincs warning emerged as: step 116 ; time 0.232 LINCS warning ralative constraint deviation after LINCS: rms 0.168368, max 4.765960 (between atoms 858 and 856) bonds that rotated more than 30 degrees: t=0.232ps : water molecular starting at atom 17660 can not be settled. check for bad contact and/or reduce the timestep. then the warning happened every step untill the programm crashed. Thanks for your discussion!! ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] reference group in constant velocity pulling, GMX 4
Dear all, I am using the pulling code in gromacs 4.0.5 with constant velocity pulling. My case is pulling protein in two opposite directions, which I do not want any other extra force acting on the protein. So I did not assign any reference group in the simulation, and I got a warning saying that: absolut coordinates is used as reference group and it will cause artifacts. According to the manual, ( 0, 0, 0 ) is used as reference group, but I still do not understand what kind of artifacts could happen. The only thing I can think of is the periodical boundary, but I am not sure, could any one have any idea? Thanks! -- Senbo Xiao PICB, Shanghai, 200031 CHINA ___ 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] gmxtest
Hi Mark, Thanks! S. On Wed, May 27, 2009 at 12:03 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Mark Abraham wrote: Simba Xiao wrote: Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. That's normal at the moment, unfortunately. Future releases of gmxtest will probably fix the non-kernel issues, and GROMACS 4.0.5 will fix the kernel issues. Sorry, I mis-remembered something. The kernel issues were caused by a hard-to-provoke bug in 3.3.x which provided the reference trajectories. GROMACS 4.0.x are fine, but the test fails because of the flawed reference values. See bugzilla 313 for details. Mark I use standard packages and everything looks find. The simulation result are good and identical to gromacs 3.3.3. But, still it annoys me with the test result. Can somebody tell how much the test matters and can somebody tell something more than the wiki tells (It dose not explain much). Well, it does explain things, but not such that a new GROMACS user can get a useful result from existing versions of gmxtest. I'll upgrade the wiki documentation if/when a gmxtest re-release happens. 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 ___ 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 -- Sen PICB, Shanghai, 200031 CHINA ___ 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] gmxtest
Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. I use standard packages and everything looks find. The simulation result are good and identical to gromacs 3.3.3. But, still it annoys me with the test result. Can somebody tell how much the test matters and can somebody tell something more than the wiki tells (It dose not explain much). Great thanks! S. -- ___ 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
[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] prolems on viewing .trr file by vmd
Dear gmx-users, When I viewed the md trajactory (*.trr) of oil/water/oil system using VMD, I found the trajactories are abnormal and as if there were forces on the molecules. However, these molecules are very far. The whole simulation is normal. How to solve this problem and obtain the normal trajactory moving? By the way, when I deal with *.gro, I used this command editconf -f test.pdb -o test.gro -c in order to make oil/water/oil system not turn into oil/water system. I do not know whether it effects the following viewing trajactory moving. I hope for your help. Thank you very much! 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] install problem
Dear gmx-users, When I parallel install gromacs-4.0.4 using my own usr. I encountered the problem. The following is my installation steps. Step 1: install lam-7.1.4 $ cd lam-7.1.4 $ ./configure --prefix=/home/xhy/software/lam-7.1.4 --without-fc --with-rsh=ssh-x $ make $ make install then adding /home/xhy/software/lam-7.1.4/bin into .bashrc file. $ source .bashrc Step 2: install fftw-3.1.2 $ cd fftw-3.1.2 $ ./configure --prefix=/home/xhy/software/fftw-3.1.2 --enable-float --enable-threads $ make $ make install then adding /home/xhy/software/fftw-3.1.2/bin, export CPPFLAGS==-I/home/xhy/software/fftw-3.1.2/include and export LDFLAGS=-L/home/xhy/software/fftw-3.1.2/lib into .bashrc file. $ source .bashrc Step 3: install gromacs-4.0.4 $ cd gromacs-4.0.4 $./configure --prefix=/home/xhy/software/gromacs-4.0.4 --exec-prefix=/home/xhy/software/gromacs-4.0.4 --enable-mpi --with-fftw3 --program-suffix=_mpi then I encountered the following errors: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. Can you help me? I hope for your answer. Thank you very much! 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] parallel install gromacs-4.0.4
Dear gmx-users, When I parallel install gromacs-4.0.4. I encountered the problem. The following is my installation steps. Step 1: install fftw-3.1.2 # cd fftw-3.1.2 # ./configure --enable-float --enable-mpi -enable-threads # make # make install Step 2: install gromacs-4.0.4 # cd gromacs-4.0.4 #./configure --enable-mpi --with-fftw3 --program-suffix=_mpi --enable-shared --enable-sse # make then I encountered the following errors: mpicc -shared .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o .libs/domdec.o .libs/domdec_con.o .libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/fftgrid.o .libs/force.o .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/pme.o .libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o .libs/tables.o .libs/tgroup.o .libs/update.o .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/gmx_fft_fftw3.o -Wl,--rpath -Wl,/usr/local/gromacs-4.0.4/src/gmxlib/.libs -Wl,--rpath -Wl,/usr/local/gromacs/lib ../gmxlib/.libs/libgmx_mpi.so -L/usr/lib64 -lxml2 -lnsl -lfftw3f -lSM -lICE -lX11 -Wl,-soname -Wl,libmd_mpi.so.5 -o .libs/libmd_mpi.so.5.0.0 ld: /usr/local/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3f.a: could not read symbols: Bad value make[3]: *** [libmd_mpi.la] Error 1 make[3]: Leaving directory `/usr/local/gromacs-4.0.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/gromacs-4.0.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/local/gromacs-4.0.4/src' make: *** [all-recursive] Error 1 How to solve these problem? Hope for your help. Thank you very much! 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] parallel install gromacs-4.0.4
Dear Mark, I do not understand your meaning. Can you explain it to me again? Thanks! 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] minimization problem
Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! 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] error range of surface tension
Hi all, I simulated the water/air system and calculated the surface tension of water by using g_energy. The following is the result: Statistics over 51 steps [ 1000.0001 thru 2000.0001 ps ], 1 data sets All averages are exact over 51 steps Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen 1417.011894.451893.74 -0.179542 -179.543 Executing 'xmgrace -nxy surface-tension.xvg ' From the result, I can obtain the water surface tension is 141.7/2=70.85 mN/m. But I want to know the error range of surface tension I calculated. Can you help me? For example in one paper, the simulated water surface tension is 70.94±2.25 mN/m. Can you tell me how to obtain the error range (as ±2.25) in the gromacs? Thank you very much! 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] charge distribution
Hi, gmx-usrs, I want to ask for a problem on the charge distribution. I simulate the sodium dodecylbenzenesulfonate and its homologues in solution using the gromos96 force field. I can not find the similar atom type as replace in the gromos96 force field . How do I define every atomic charge? I have the mulliken charge distribution and ESP charge from the quantum calculation. Should I employ them? Can you give me some advice? 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] charge distribution
Dear Justin, For sodium dodecylbenzenesulfonate(C12H25C6H4SO3Na), the charges of S and O in S03- , I cannot find the suitable charge. Forthermore, the carbon in benzene connecting the SO3- is setted to be zero, I think that there may be questionable. The polarization of SO3- is very large. what do you think so? 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] surface simulation
Hi, all gmx-users, I was simulating a CCl4 surface system. I encounter some problems. I hope for your help. First I built a 3x3x3 nm3 CCl4 box, then solved it into a 3x3x15 box in order to form gas/CCl4/gas surface system. After simulating in NVT, two CCl4 molecules run away to the gas phase. I want to know how to control CCl4 not to run to gas phase. I used the gromos96 force field. Can you help me? I expect your answer. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CCl4 parameters problem
Hi, all gmx-users, I obtained the gromos96.1 itp file of CCl4 from the PRODRG program and I modified it to agree with the ffG53a6.itp force field parameters. Please see the following, [ moleculetype ] ; Name nrexcl CL4 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CLCL4 1 CL4 CL1 1 -0.062 35.4530 2 CCL4 1 CL4 CT 10.248 12.0110 3 CLCL4 1 CL4 CL4 1 -0.062 35.4530 4 CLCL4 1 CL4 CL2 1 -0.062 35.4530 5 CLCL4 1 CL4 CL3 1 -0.062 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.176 810.00.176 810.0 ;CT CL1 2 3 20.176 810.00.176 810.0 ;CT CL4 2 4 20.176 810.00.176 810.0 ;CT CL2 2 5 20.176 810.00.176 810.0 ;CT CL3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2109.5 618.0109.5 618.0 ; CL1 CT CL4 1 2 4 2109.5 618.0109.5 618.0 ; CL1 CT CL2 1 2 5 2109.5 618.0109.5 618.0 ; CL1 CT CL3 3 2 4 2109.5 618.0109.5 618.0 ; CL4 CT CL2 3 2 5 2109.5 618.0109.5 618.0 ; CL4 CT CL3 4 2 5 2109.5 618.0109.5 618.0 ; CL2 CT CL3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 35.3 334.8 35.3 334.8 ; impCT CL1 CL4 CL2 However, when I ran the grompp program, it pointed out the following the warning WARNING 1 [file ccl4.top, line 25]: Too few parameters on line (source file toppush.c, line 1499) I had a check the CCl4 parameters again and did not find the parameter lost. I want to know why the warning occurs? I hope for your help! Thanks! 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CCl4 parameters
Hi, Justin, This is my CCl4.top file. ; ; File 'ccl4.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 9 08:18:55 2008 ; ; This is your topology file ; God is a DJ (Faithless) ; ; Include forcefield parameters #include ffG53a6.itp #include ccl4.itp ; Include generic topology for ions #include ions.itp [ system ] ; Name Pure CL4 [ molecules ] ; Compound#mols CL4169 ~ What does it lose? Please give me further suggestion. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] surface simulation
Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl4, can I control the CCl4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dynamics with toluene as solvent
I think you can use The Dundee PRODRG sever to generate toluene structure and topology for gromacs, but use it with care. On 9/21/07, Eva Santos [EMAIL PROTECTED] wrote: Hello everyone, I need to do some molecular dynamics, using gromos96 force field, with toluene as solvent. I have found an article which mentions the existence of an all-atom model for this solvent parametrized under gromos96 ( J.Phys. Chem. B 2004, 108, 11774-11781). However I have not managed to find the gromacs coordinate files, the topology files, etc. to use it in gromacs. Do they exist anywhere? Regards, Eva ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
