Re: [gmx-users] Using Charmm FF with implicit solvent on gromacs
Hi! Currently it is not possible to use GBSW in Gromacs. As you noted, there are three GB-models available (Still,HCT,OBC), that can be run using plain cutoffs (or no cutoffs at all, using the optimized all-vs-all kernels). Currently there is unfortunately no work being done to extend the range of implicit solvent models available. However, we have had some promising results with the combination of CHARMM FF + CMAP + OBC, as discussed in the 2010 JCTC paper. Cheers /Per 18 nov 2010 kl. 22.49 skrev César Ávila: Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models Still Hawkins-Cramer-Truhlar (HCT) Onufriev-Bashford-Case (OBC) The charmm FF has been extensively tested with the GBSW* implementation (in Charmm program) for which the backbone phi/psi cross-term (CMAP) and the atomic input radii were specifically optimized (Chan, Im and Brooks, JACS, 2006). Is there a way to perform the same calculation on gromacs? * W. Im, M.S. Lee, and C.L. Brooks III Generalized Born Model with a Simple Smoothing Function. J. Comput. Chem. 24:1691-1702 (2003). -- 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] Pairwise forces
Dear all, I know similar topics have already been discussed, but there is a question regarding pairwise forces that could not be resolved by reading the mailing list. Our group has already done some rather long simulations and according to the script files forces are written every 1 steps and can be accessed via trjconv with -cf option that assigns each atom a temperature factor. I was wondering if that is the way gromacs stores the forces in the trajectory file. Or are the temperature factors calculated from other (maybe pairwise) forces? I also had a look at FDA gromacs that is able to write out pairwise forces, but unfortunately it falls back on the rather slow gromacs routines and we want to avoid rerunning our simulations if possible. Sincerely, Reiner -- 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] Role of epsilon_rf in implicit solvation
Dear users, I've got yet another question about the implicit solvent models used in Gromacs. I saw in some simulations that epsilon_rf was set to 0 meaning infinite dielectric constant. The manual is not clear about this, since it is mentioned in combination with reaction field only. So is this epsilon_rf also used in combination in implicit solvent models regarding the dielectric constant beyond cut-off? If yes, what would be an appropriate value for this constant? Best regards, Christian -- Christian Mücksch Department of Physics TU Kaiserslautern Erwin Schrödinger Straße 67663 Kaiserslautern Germany Phone: +49 (0)631 205 4287 Fax: +49 (0)631 205 4965 Email: mueck...@rhrk.uni-kl.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Role of epsilon_rf in implicit solvation
Hi! It would be nice to have reaction-field for GB as well, but currently this is not the case. The polarisation energy is scaled using (1.0/epsilon_r - 1.0/gb_epsilon_solvent) always, epsilon_rf is never used. Cheers /Per 19 nov 2010 kl. 12.30 skrev Christian Mücksch: So is this epsilon_rf also used in combination in implicit solvent models regarding the dielectric constant beyond cut-off? If yes, what would be an appropriate value for this constant? -- 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] question about simualtion of CNT from a rookie
Dear all, I am trying to study an infinite length CNT in SPC water box under NPT using gromacs 4.5.3. The axis of CNT is along Z direction. The options pbc = xyz and periodic_molecules = yes are included in all mdp files. The whole system was minimized first, followed by an NVT simulation. The structure was fine, at least when visualized with VMD. Then I ran an NPT simulation with weak restraint on CNT. The pressure coupling options are set as following ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 2.0 0.0 ; time constant, in ps ref_p = 1.0 0.0 ; reference pressure, in bar compressibility = 4.5e-5 0.0; isothermal compressibility of water, bar^-1 And the final structure was also fine. But then I removed the constraint, and tried to run a long time simulation under NPT, the whole system exploded in several ps. I have not figured out what was wrong in my calculation. Can anyone give me a suggestion? Ye MEI -- 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] noxvgr
Hi, Suppose when I use gyrate, I want the output to be the eps, when I tried -noxvgr -w sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- 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] noxvgr
#ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use -xvg none in the command line. If you just want an .eps output file of the plot, use the normal XmGrace formatting (leave the command line -xvg alone) and save the output in that format. XmGrace should be capable of saving an .eps, and if not, you can take whatever image file format it gives you into Gimp and convert it. -Justin sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] noxvgr
I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use -xvg none in the command line. If you just want an .eps output file of the plot, use the normal XmGrace formatting (leave the command line -xvg alone) and save the output in that format. XmGrace should be capable of saving an .eps, and if not, you can take whatever image file format it gives you into Gimp and convert it. -Justin sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] noxvgr
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/19/2010 03:03 PM, #ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, when I tried -noxvgr -w sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? If you want to use gnuplot for the plotting you have to set the corresponding comment character set datafile commentchars #...@! Put this line in your $HOME/.gnuplot file that is read every time you start gnuplot, or set it every time you want to plot xvg files and you will have no trouble. /Flo Thanks and best, lina - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzmiD4ACgkQLpNNBb9GiPmTvwCgpvTeF6kDM6Ri4HhtG15fwUfW kqIAniWR0aNfFvZ+OQDxx8z0kgbygAen =JtXr -END PGP SIGNATURE- -- 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] noxvgr
#ZHAO LINA# wrote: I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Exporting to different formats is not done with Save As but rather Print (using Print Setup to choose the proper format). Simply saving your plot creates an XmGrace file that only it can load. -Justin Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use -xvg none in the command line. If you just want an .eps output file of the plot, use the normal XmGrace formatting (leave the command line -xvg alone) and save the output in that format. XmGrace should be capable of saving an .eps, and if not, you can take whatever image file format it gives you into Gimp and convert it. -Justin sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] noxvgr
It works (cool). Thanks for both of you. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Exporting to different formats is not done with Save As but rather Print (using Print Setup to choose the proper format). Simply saving your plot creates an XmGrace file that only it can load. -Justin Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:15 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] noxvgr #ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use -xvg none in the command line. If you just want an .eps output file of the plot, use the normal XmGrace formatting (leave the command line -xvg alone) and save the output in that format. XmGrace should be capable of saving an .eps, and if not, you can take whatever image file format it gives you into Gimp and convert it. -Justin sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mpdboot and mpirun hangs (not crashing)
Hi, I am trying to run my production run with mpirun and this hangs (basically stop writing any files). The processes continue to run without any output. I have to kill and restart which again hangs after some time. Does anyone have any problems with this? what I am doing is mpdboot -n 1 -f NODEFILE nohup mpirun -np 12 mdrun_mpi -v -deffnm protein-prod what could have been going wrong here?? What could I try 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
Re: [gmx-users] mpdboot and mpirun hangs (not crashing)
On 20/11/2010 2:57 AM, X Rules wrote: Hi, I am trying to run my production run with mpirun and this hangs (basically stop writing any files). The processes continue to run without any output. I have to kill and restart which again hangs after some time. Does anyone have any problems with this? what I am doing is mpdboot -n 1 -f NODEFILE nohup mpirun -np 12 mdrun_mpi -v -deffnm protein-prod what could have been going wrong here?? What could I try Probably something about your MPI installation, or perhaps network file system, is poorly configured, but it's impossible for us to guess better with the information we have. You should try different things and see what works and what does not. 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/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] Pairwise forces
On 19/11/2010 10:15 PM, Reiner Ribarics wrote: Dear all, I know similar topics have already been discussed, but there is a question regarding pairwise forces that could not be resolved by reading the mailing list. Our group has already done some rather long simulations and according to the script files forces are written every 1 steps and can be accessed via trjconv with -cf option that assigns each atom a temperature factor. I was wondering if that is the way gromacs stores the forces in the trajectory file. Or are the temperature factors calculated from other (maybe pairwise) forces? A trajectory file of T frames of N atoms containing only forces is simply T sets of 3*N numbers interleaved with some per-frame header information. There is no way to decompose anything after the fact. g_traj works from those forces. I also had a look at FDA gromacs that is able to write out pairwise forces, but unfortunately it falls back on the rather slow gromacs routines and we want to avoid rerunning our simulations if possible. Anything that computes pairwise forces will necessarily be slow, or a memory-hog, or both. 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/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] mpdboot and mpirun hangs (not crashing)
I am trying to check some of these issues. thanks for your help Date: Sat, 20 Nov 2010 03:38:08 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] mpdboot and mpirun hangs (not crashing) Message body On 20/11/2010 2:57 AM, X Rules wrote: Hi, I am trying to run my production run with mpirun and this hangs (basically stop writing any files). The processes continue to run without any output. I have to kill and restart which again hangs after some time. Does anyone have any problems with this? what I am doing is mpdboot -n 1 -f NODEFILE nohup mpirun -np 12 mdrun_mpi -v -deffnm protein-prod what could have been going wrong here?? What could I try Probably something about your MPI installation, or perhaps network file system, is poorly configured, but it's impossible for us to guess better with the information we have. You should try different things and see what works and what does not. 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/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] mutiple dihedral terms
Hi, I have a molecule consisting of 4 atoms 1-2-3-4 . The paper parameterizing the molecule has reported combination of following multiple set of dihedral terms by fitting the dihedral angle distributions of this tetra-atomic molecule : theta0 K n 180 1.96 1 0 0.18 2 0 0.333 00.12 4 Now, I was trying to incorporate this dihedral terms in my gromacs topology file: My question is , is it possible to use Proper dihedral angles four time for the same dihdral angles : i.e If I write the dihedral part of topology file in the following way, will it be OK so that Gromacs will add them up ? [dihedrals] 1 2 3 4 1180.001.96 1 1 2 3 4 1 00.18 2 1 2 3 4 1 00.33 3 1 2 3 4 1 00.12 4 Or, will it consider only the last one ? If it is not the case, Am I supposed to convert them into Ryckert Bellman type and sum them up ? Any suggestion will be helpful. Sanku -- 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] mutiple dihedral terms
Sanku M wrote: Hi, I have a molecule consisting of 4 atoms 1-2-3-4 . The paper parameterizing the molecule has reported combination of following multiple set of dihedral terms by fitting the dihedral angle distributions of this tetra-atomic molecule : theta0 K n 180 1.96 1 0 0.18 2 0 0.333 00.12 4 Now, I was trying to incorporate this dihedral terms in my gromacs topology file: My question is , is it possible to use Proper dihedral angles four time for the same dihdral angles : i.e If I write the dihedral part of topology file in the following way, will it be OK so that Gromacs will add them up ? [dihedrals] 1 2 3 4 1180.001.96 1 1 2 3 4 1 00.18 2 1 2 3 4 1 00.33 3 1 2 3 4 1 00.12 4 Or, will it consider only the last one ? They are additive. Surely this is in the manual somewhere. -Justin If it is not the case, Am I supposed to convert them into Ryckert Bellman type and sum them up ? Any suggestion will be helpful. Sanku -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] question regarding to PMF calculation between 2 plates
Dear GROMACS users, I have a question for calculating the potential of mean force between 2 plates (i.g., graphene) in water. It is not technically as simple as it seem. I found this question has been asked many times (I sum them up in the bottom of this note, so maybe it will be helpful for someone with similar question in future) but I cannot see a clear answer completely solving the problem. Information in the manual is quite limited on this topic as well. There are two ways I can see to do the calculation: 1. umbrella sampling; 2. free energy perturbation (JACS, 2005, 127, 3556). Both of them, however, need to deal with 2 questions first in order to get any meaningful result: 1. keep the plates to be really plates (flat surface); 2. inhibit plate rotation. There are 3 ways that come into my mind to solve these 2 problems, but none of them works as I tried. (Similar idea has been suggested in the previous posts regarding to the problem.) I am using a simple NPT system in the free energy perturbation scheme, because it is physically more meaningful and simpler to test than umbrella potential. But problem comes from the 3 method I tried: 1) Merely constructing a really complicated itp file with bond, angle, dihedral, imp dihedral cannot easily maintain a planar plate. Rotation of the plates is not easy to deal with, which I still don't have any idea yet. (Someone suggested other methods rather than this one in the previous post.) 2) Freezing all plates will make the plates do what they should do, but there is problem with the pressure coupling according to the manual. GMX 4.0.x wouldn't work as specified in the manual. GMX 3.3.3 works as it seems but the system is very easy to blow up. 3) Use position RESTRAINT on all atoms on the plates in XYZ direction (basically fixing them in the initial position) as suggested in previous posts. As an example: --- [ position_restraints ] ; ai funct fc 1 195000 95000 95000 2 195000 95000 95000 3 195000 95000 95000 4 195000 95000 95000 every atom in the plates However, or small force constant, the plate won't be maintained. For large force constant (the above example), the system will easily blow up even with time step of 1fs. For sure, once we have too large vibration in the system, an even smaller time step is required. Then the efficiency is going to be really really low. (To provide further details: I minimize the system with both steep and cg first and run the 400 ps NVT(Nose) run before the NPT (Parrinello, isotropic or semiisotropic) run. The test system is fairly small: 570 waters (SPC/E) with 2 plates of graphene (60 atoms each, amber parameters). So there should not be problem with the equilibration. I tuned the force constant in the restraint to see whether the plate change or not.) I will really appreciate it if someone can suggest some way out or where my problem is in the simulation. Is it the right way of restraining the system? Is there better way of doing this? It will be great if discussions coming along. Thank you in advanced for your help! (There has been tons of paper doing this with some other package, I am sure GROMACS can do it. I am just not the person who can figure this out.) Thanks, Zhe Links for the previous representative post related: http://lists.gromacs.org/pipermail/gmx-users/2010-February/048615.html http://lists.gromacs.org/pipermail/gmx-users/2010-January/048326.html http://lists.gromacs.org/pipermail/gmx-users/2009-December/047696.html -- 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] disparity in RMSD calculation
On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel sun...@mailhost.tifr.res.inwrote: Dear Users, I calculated RMSD for a trajectory with same reference structure using GROMACS and VMD. I observed completely difference plots for the same data. Please see the attached file. What could be the cause for this disparity? it is hard to predict what is causing the disparity without what you typed in the terminal, and your system. Perhaps check if you've removed the periodic boundary conditions when calculating the rmsd in gmx by invoking -nopbc option. Greg Thanks for any suggestion. Sunita -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] disparity in RMSD calculation
On Sat, 20 Nov 2010 01:13:51 -0500, Yongchul Chung wrote On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel sun...@mailhost.tifr.res.in wrote: Dear Users, I calculated RMSD for a trajectory with same reference structure using GROMACS and VMD. I observed completely difference plots for the same data. Please see the attached file. What could be the cause for this disparity? it is hard to predict what is causing the disparity without what you typed in the terminal, and your system. Perhaps check if you've removed the periodic boundary conditions when calculating the rmsd in gmx by invoking -nopbc option. Still, am getting the same plot in gmx even after removal of periodic boundary conditions. Visual observation of trajectory on VMD is more similar to the RMSD am getting from VMD. My worry is that why gmx is not giving the similar result. Thanks Greg. Any suggestion will be appreciated. Sunita Greg Thanks for any suggestion. Sunita -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. Sunita Patel - Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 45 - -- 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
