Hi, Oh, I see. Yes that feature turns off both kinds of non-bonded interactions. Then there is nothing useful for what you want.
Mark On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan <davtyan.a...@gmail.com> wrote: > Hi Mark, > > I apologize if I did not describe my problem correctly the first time, but > I need the VdW interactions to stay on between all atoms at all times. I > only need to turn off the electrostatic interactions between water and > proteins. > > Thanks, > > Aram > > Hi, > > > > You've described the feature correctly. Whether it is useful in a study > > design is another matter :-) > > > > Mark > > > > On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hi Mark, > > > > > > I am not sure I understood. If I for example say "energygrp-excl = > > Protein > > > Water" would not I turn off all the non-bonded interactions between > water > > > and protein? Or did you mean something else? > > > > > > Thanks, > > > > > > Aram > > > > > > > > > > Hi, > > > > > > > > In the group scheme you can turn on energy-group exclusions to get > this > > > > working, but of course all of those states are sampling unphysical > > things > > > > from a broken forcefield. That can be OK, but you will have to be > able > > to > > > > defend that claim. > > > > > > > > Mark > > > > > > > > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.a...@gmail.com > > > > > > wrote: > > > > > > > > > Hello, > > > > > > > > > > I am running simulations of two protein domains in tip4p water and > > > 0.15M > > > > > salt concentration that contain up to 650,000 atoms total. The > > protein > > > > > domains are separated from each other at the start of each > simulation > > > > and I > > > > > am measuring how the distance between them changes over time. > > > > > > > > > > Now, I need to do the same simulations, but with electrostatics > > between > > > > > proteins and water turned off (with water-water, protein-protein, > > > > > ion-water, ion-protein electrostatics remaining). Then I need to > > repeat > > > > > that, but additionally turning off electrostatics between the two > > > > domains. > > > > > Water-water, ion-water, ion-protein, intra-domain electrostatics > > should > > > > > remain on. > > > > > > > > > > What will be the best way to do this? > > > > > > > > > > I am using CHARMM27 force field and the following settings to run > the > > > > > production simulations: > > > > > > > > > > integrator = md > > > > > dt = 0.002 > > > > > nsteps = 1000000 ; 2ns > > > > > nstlog = 1000 > > > > > nstxout = 5000 > > > > > nstvout = 5000 > > > > > nstfout = 5000 > > > > > nstcalcenergy = 100 > > > > > nstenergy = 1000 > > > > > ; > > > > > cutoff-scheme = Verlet > > > > > nstlist = 20 > > > > > rlist = 1.2 > > > > > coulombtype = pme > > > > > rcoulomb = 1.2 > > > > > vdwtype = Cut-off > > > > > vdw-modifier = Force-switch > > > > > rvdw_switch = 1.0 > > > > > rvdw = 1.2 > > > > > ; > > > > > tcoupl = Nose-Hoover > > > > > tc_grps = Protein Non-Protein > > > > > tau_t = 1.0 1.0 > > > > > ref_t = 300.0 300.0 > > > > > ; > > > > > pcoupl = Parrinello-Rahman > > > > > pcoupltype = isotropic > > > > > tau_p = 5.0 > > > > > compressibility = 4.5e-5 > > > > > ref_p = 1.0 > > > > > ; > > > > > constraints = h-bonds > > > > > constraint_algorithm = LINCS > > > > > continuation = yes > > > > > ; > > > > > nstcomm = 100 > > > > > comm_mode = linear > > > > > comm_grps = Protein Non-Protein > > > > > ; > > > > > refcoord_scaling = com > > > > > > > > > > > > > > > I have tried to use the energy groups (energygrp-table) to specify > > > > > interaction tables between water and protein, where I would set the > > > > > electrostatic potential to zero. However, given that > energygrp-table > > > and > > > > > Varlet cutoff-scheme are incompatible, I could not make it work. > But > > it > > > > is > > > > > possible that I did something wrong. > > > > > > > > > > Thank you in advance, > > > > > > > > > > Aram > > > > > -- > > > > > 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. > > > > > > > > > ------------------------------ > > > > -- > > 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. > > > > End of gromacs.org_gmx-users Digest, Vol 163, Issue 69 > > ****************************************************** > > > > > > -- > Aram Davtyan, Ph.D. > Center for Theoretical Biological Physics > Rice University > E-mail: adavt...@rice.edu <adavt...@uchicago.edu> > Phone: (919)265-8369 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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