[gmx-users] Re: energy conservation: shift vs shifted user potential
Ok, that didn't help me much. Of course I changed both, potential and force to shifted ones. And sure I used a little fortran code to generate the tables -- I have found the problem: I thought GROMACS would ignore the table values above the cutoff distance, but it does not. I added zeros and now it works. Thanks anyway Anja > - Original Message - > - Original Message - > From Mark Abraham > Date Sat, 09 Jun 2012 12:59:17 +1000 > To Discussion list for GROMACS users > Subject Re: [gmx-users] Re: Re: energy conservation: shift vs > shifted user potential > On 9/06/2012 2:05 AM, Anja Kuhnhold wrote: > > Ok, I try to explain it again :) > > I know the format of the user tables (x, f(x), -f'(x), g(x), -g'(x), > h(x), -h'(x); > > f is coulomb, g dispersion, h repulsion). > > For testing the simple cut-off version, my table looks like the > > example in the installation. > > So I run a simulation with vdwtype=cut-off > > and the same with vdwtype=user. > > The results are the same. > > > > The problem is, that I want to use shifted forces and potentials > within my tables. > > (Aim is better energy conservation) > > In the manual (ch. 4.1.5) is explained how the shift functions > > for forces and potentials have to be. > > So for -g(x) and h(x) I use the potential from the manual, Phi, with > alpha=6 and 12, respectivly. > > And for g'(x) and -h'(x) I use the shifted force from the manual, > Fs, with alpha=6 and 12, respectivly. > > But when I run the simulation with this table on the one hand > > and with vdwtype=Shift on the other hand, > > the results are not comparable, mostly the energy is not conserved > by using the table. > > The force is the negative derivative of the potential. If you change > only the force columns then you have made the interaction piecewise > discontinuous at every segment. So when GROMACS uses both the values > and > derivatives to convert your table into the internal format used > (section > 6.7.1), it comes up with junk. There should be a warning printed if > the > force column is not close enough to the numerical derivative of the > potential column, but maybe this change is close enough that you avoid > > that. Anyway, this makes energy basically impossible to conserve. You > > should generate all your table values from the actual function you > wish > to implement, e.g. with a spreadsheet or scripting language. > > Mark > > > > > Can you follow me? > > > > Anja > > > > > > > > - Ursprüngliche Nachricht - > > Von: gmx-users-requ...@gromacs.org > > Datum: Freitag, Juni 8, 2012 15:55 > > Betreff: gmx-users Digest, Vol 98, Issue 52 > > An: gmx-users@gromacs.org > > > >> - Ursprüngliche Nachricht - > >> Von Mark Abraham > >> Datum Fri, 08 Jun 2012 23:40:35 +1000 > >> An Discussion list for GROMACS users > >> Betreff Re: [gmx-users] Re: energy conservation: shift vs shifted user > >> potential > >> On 8/06/2012 5:59 PM, Anja Kuhnhold wrote: > >>> Hello all, > >>> > >>> can someone give me a hint, please? > >>> Do you need more information? > >>> Has anyone had a similar problem. > >>> > >>> I really need to figure that out, because I will simulate other systems > >>> which can be run only with user tables. > >>> > >>> Anja > >>> > >>> > >>> > >>> - > >>>> - Original Message - > >>>> - Original Message - > >>>> From Anja Kuhnhold > >>>> Date Wed, 06 Jun 2012 15:07:40 +0200 > >>>> To gmx-users@gromacs.org > >>>> Subject [gmx-users] energy conservation: shift vs shifted user potential > >>>> Dear gmx-users, > >>>> > >>>> I have a problem concerning energy conservation when using user > >>>> potentials (tables). > >>>> I'm using gromacs 4.5.4 > >>>> I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 > >>>> chains a 10 beads in a 26x26x26 periodic box). > >>>> > >>>> I tried different vdwtypes (cutoff always 3.24): > >>>> The cut-off version does not conserve energy -- okay. > >>>> The shift and switch versions conserve energy -- fine. > >>>> > >>>> Now I wanted to do the same with user tables: > >>>> Simple Lennard-Jones table gives really the same re
[gmx-users] Re: Re: energy conservation: shift vs shifted user potential
Ok, I try to explain it again :) I know the format of the user tables (x, f(x), -f'(x), g(x), -g'(x), h(x), -h'(x); f is coulomb, g dispersion, h repulsion). For testing the simple cut-off version, my table looks like the example in the installation. So I run a simulation with vdwtype=cut-off and the same with vdwtype=user. The results are the same. The problem is, that I want to use shifted forces and potentials within my tables. (Aim is better energy conservation) In the manual (ch. 4.1.5) is explained how the shift functions for forces and potentials have to be. So for -g(x) and h(x) I use the potential from the manual, Phi, with alpha=6 and 12, respectivly. And for g'(x) and -h'(x) I use the shifted force from the manual, Fs, with alpha=6 and 12, respectivly. But when I run the simulation with this table on the one hand and with vdwtype=Shift on the other hand, the results are not comparable, mostly the energy is not conserved by using the table. Can you follow me? Anja - Ursprüngliche Nachricht - Von: gmx-users-requ...@gromacs.org Datum: Freitag, Juni 8, 2012 15:55 Betreff: gmx-users Digest, Vol 98, Issue 52 An: gmx-users@gromacs.org > - Ursprüngliche Nachricht - > Von Mark Abraham > Datum Fri, 08 Jun 2012 23:40:35 +1000 > An Discussion list for GROMACS users > Betreff Re: [gmx-users] Re: energy conservation: shift vs shifted user > potential > On 8/06/2012 5:59 PM, Anja Kuhnhold wrote: > > Hello all, > > > > can someone give me a hint, please? > > Do you need more information? > > Has anyone had a similar problem. > > > > I really need to figure that out, because I will simulate other systems > > which can be run only with user tables. > > > > Anja > > > > > > > > - > >> - Original Message - > >> - Original Message - > >> From Anja Kuhnhold > >> Date Wed, 06 Jun 2012 15:07:40 +0200 > >> To gmx-users@gromacs.org > >> Subject [gmx-users] energy conservation: shift vs shifted user potential > >> Dear gmx-users, > >> > >> I have a problem concerning energy conservation when using user > >> potentials (tables). > >> I'm using gromacs 4.5.4 > >> I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 > >> chains a 10 beads in a 26x26x26 periodic box). > >> > >> I tried different vdwtypes (cutoff always 3.24): > >> The cut-off version does not conserve energy -- okay. > >> The shift and switch versions conserve energy -- fine. > >> > >> Now I wanted to do the same with user tables: > >> Simple Lennard-Jones table gives really the same results as the > >> cut-off version -- good. > >> > >> But if I use a table with shifted Lennard-Jones potential it is not > >> comparable to the shift version > >> and the energy is not conserved -- ? > >> > >> I use a shift function as written in the manual (chapter 4.1.5) -- > >> there must be a factor alpha added in the constants A and B -- > >> (r1=0). > >> > >> The parameters are the same for shift version and shifted user version. > >> > >> Has someone an idea why the shifted user potential doesn't work in > >> this way? > > We've no real idea what you've done... manual 6.7.2 describes the > required format and there are (unshifted) examples in your > installation > under $GMXLIB/share/top/table*.xvg. > > Makr > > >> > >> Here is the mdp: > >> > >> > >> integrator = md-vv > >> dt = 0.0035 > >> nsteps = 1000 > >> nstxout= 1 > >> nstvout= 1 > >> nstfout= 1 > >> nstlog = 1 > >> ns_type= grid > >> pbc= xyz > >> rvdw = 3.24 > >> rlist = 3.6 > >> tcoupl = no > >> tc-grps= System > >> tau_t = 2.0 > >> ref_t = 127.2717 > >> vdwtype= user;Shift > >> rcoulomb = 3.6;2.24;1.12 > >> coulombtype= Cut-off > >> rvdw-switch= 0.0 > >> > >> energygrps = bead > >> energygrp_table= bead bead > >> > >> > >> Thanks in advance > >> Anja > >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: energy conservation: shift vs shifted user potential
Hello all, can someone give me a hint, please? Do you need more information? Has anyone had a similar problem. I really need to figure that out, because I will simulate other systems which can be run only with user tables. Anja - > - Original Message - > - Original Message - > From Anja Kuhnhold > Date Wed, 06 Jun 2012 15:07:40 +0200 > To gmx-users@gromacs.org > Subject [gmx-users] energy conservation: shift vs shifted user potential > Dear gmx-users, > > I have a problem concerning energy conservation when using user > potentials (tables). > I'm using gromacs 4.5.4 > I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 > chains a 10 beads in a 26x26x26 periodic box). > > I tried different vdwtypes (cutoff always 3.24): > The cut-off version does not conserve energy -- okay. > The shift and switch versions conserve energy -- fine. > > Now I wanted to do the same with user tables: > Simple Lennard-Jones table gives really the same results as the > cut-off version -- good. > > But if I use a table with shifted Lennard-Jones potential it is not > comparable to the shift version > and the energy is not conserved -- ? > > I use a shift function as written in the manual (chapter 4.1.5) -- > there must be a factor alpha added in the constants A and B -- > (r1=0). > > The parameters are the same for shift version and shifted user version. > > Has someone an idea why the shifted user potential doesn't work in > this way? > > Here is the mdp: > > > integrator= md-vv > dt= 0.0035 > nsteps= 1000 > nstxout = 1 > nstvout = 1 > nstfout = 1 > nstlog= 1 > ns_type = grid > pbc = xyz > rvdw = 3.24 > rlist = 3.6 > tcoupl= no > tc-grps = System > tau_t = 2.0 > ref_t = 127.2717 > vdwtype = user;Shift > rcoulomb = 3.6;2.24;1.12 > coulombtype = Cut-off > rvdw-switch = 0.0 > > energygrps= bead > energygrp_table = bead bead > > > Thanks in advance > Anja > -- 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] energy conservation: shift vs shifted user potential
Dear gmx-users, I have a problem concerning energy conservation when using user potentials (tables). I'm using gromacs 4.5.4 I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 chains a 10 beads in a 26x26x26 periodic box). I tried different vdwtypes (cutoff always 3.24): The cut-off version does not conserve energy -- okay. The shift and switch versions conserve energy -- fine. Now I wanted to do the same with user tables: Simple Lennard-Jones table gives really the same results as the cut-off version -- good. But if I use a table with shifted Lennard-Jones potential it is not comparable to the shift version and the energy is not conserved -- ? I use a shift function as written in the manual (chapter 4.1.5) -- there must be a factor alpha added in the constants A and B -- (r1=0). The parameters are the same for shift version and shifted user version. Has someone an idea why the shifted user potential doesn't work in this way? Here is the mdp: integrator = md-vv dt = 0.0035 nsteps = 1000 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 ns_type = grid pbc = xyz rvdw= 3.24 rlist = 3.6 tcoupl = no tc-grps = System tau_t = 2.0 ref_t = 127.2717 vdwtype = user;Shift rcoulomb= 3.6;2.24;1.12 coulombtype = Cut-off rvdw-switch = 0.0 energygrps = bead energygrp_table = bead bead Thanks in advance Anja -- 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] cutoffs
Hi, is it possible to have different cutoffs for different interactions? Best regards Anja -- 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] plateau in msd (glass transition); ref_t
Hi everyone, I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain in a 26.6^3 box with pbc) with LJ and FENE potentials. I calculate the mean-square-displacement for different temperatures. For T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass transition)- but there is none. The curve for T=0.46 is similar to the one for T=1.0 (above glass transition) with only a small shift to lower values- but no plateau. My .mdp-files look as follows: integrator = md-vv dt = 0.0035 nsteps = 100 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 ns_type = grid pbc = xyz periodic_molecules = yes rvdw = 1.12 rlist = 1.3 tcoupl = nose-hoover tc-grps = System tau_t = 20 ref_t = 55.32 vdwtype = Shift rcoulomb = 1.12 coulombtype = Reaction-Field-zero epsilon_rf = 0 I have 6 of these files, where only nsteps and nst*out are changed by multiplying them by 10 (so I get overlapping intervals for the msd). Is the ref_t correct? The results in the md.log file say T is about 89. Why do I not get a plateau? What did I not consider? Thanks in advance. Anja -- 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] plateau in msd (glass transition); ref_t
Hi everyone, I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain in a 26.6^3 box with pbc) with LJ and FENE potentials. I calculate the mean-square-displacement for different temperatures. For T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass transition)- but there is none. The curve for T=0.46 is similar to the one for T=1.0 (above glass transition) with only a small shift to lower values- but no plateau. My .mdp-files look as follows: integrator = md-vv dt = 0.0035 nsteps = 100 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 ns_type = grid pbc = xyz periodic_molecules = yes rvdw= 1.12 rlist = 1.3 tcoupl = nose-hoover tc-grps = System tau_t = 20 ref_t = 55.32 vdwtype = Shift rcoulomb= 1.12 coulombtype = Reaction-Field-zero epsilon_rf = 0 I have 6 of these files, where only nsteps and nst*out are changed by multiplying them by 10 (so I get overlapping intervals for the msd). Is the ref_t correct? The results in the md.log file say T is about 89. Why do I not get a plateau? What did I not consider? Thanks in advance. Anja -- 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
