Thank you professor Justin. Firstly, I get a true trajectory (stress.trr) from Gromacs 5.0.5 besides the water.gro, water.top, and nvt.mdp files. Then read the these files with a custom Gromacs 4.5.5 to calculate local pressure: grompp_LS -f nvt.mdp -c water.gro -p water.top -o topol.tpr
mdrun_LS -s topol.tpr -rerun stress.trr -localsgrid 0.2 -lsgridx 1 -lsgridy 1 The problem is when I set the box dimensions to be decimals (say 4.5 nm) in water.gro, the mdrun_LS does not work. After changing them to be integers (such as 4 or 5 nm), the mdrun_LS works. Will this affect the results? I am using the true trajectory (stress.trr) in -rerun command. What roles do the .gro and .mdp files play in the -rerun since positions and velocities of atoms at each frame are available in the .trr file? Best wishes,Xiaohui > Date: Thu, 20 Aug 2015 18:52:05 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 > or 1 for Polarization. > > > > On 8/20/15 6:05 PM, 折晓会 wrote: > > Thank you professor Justin! I solved this error which comes from the > > decimals of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 > > nm3 and the local pressure calculation does not work, but after I change > > them to be integers 4*4*16 nm3 in the gro file, the simulation works. It is > > strange for me. I do not know why. > > > > I fail to see how making the box smaller solves a "box too small" error, and > moreover, making changes like this is going to affect the results. Don't > consider this a solution. Probably an indication of a bug. So you're just > reading in a .gro file? Does a single coordinate file trigger the error > before, > or was that from an actual trajectory? > > -Justin > > > Best wishes, > > Xiaohui > > > >> Date: Thu, 20 Aug 2015 16:44:58 -0400 > >> From: jalem...@vt.edu > >> To: gmx-us...@gromacs.org > >> Subject: Re: [gmx-users] Incorrect number of parameters - found 3, > >> expected 1 or 1 for Polarization. > >> > >> > >> > >> On 8/20/15 4:01 PM, 折晓会 wrote: > >>> Thank you professor Justin! I solved this error with your suggestion. > >>> > >>> When I use mdrun -rerun to calculate the local pressure, another error > >>> occurs: > >>> > >>> Fatal error: > >>> Rerun trajectory frame step 600000 time 600.000000 has too small box > >>> dimensions > >>> > >>> What does this mean? > >>> > >> > >> It means your box is too small. What are the box dimensions in that > >> frame, and > >> what are the cutoffs you are using? > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 629 > >> University of Maryland, Baltimore > >> 20 Penn St. > >> Baltimore, MD 21201 > >> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> ================================================== > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > >> a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
