Hi, I have a system containing two graphene sheets (with residue names GR1 and GR2, respectively) plus some liquid. I would like to hold the two graphene sheets fixed in space and observe the dynamics of the liquid around it.
To hold the graphene sheets fixed in space, I used freeze groups: freezegrps = GR1 GR2 freezedim = Y Y Y Y Y Y ; freeze x, y & z directions This indeed holds the sheets fixed in space, just as I want. However, the pressure increases dramatically, from about 10^3 bar with no frozen atoms to about 10^29 bar when the graphene sheets are frozen. I noticed that the manual says (http://manual.gromacs.org/current/online/mdp_opt.html#neq): "To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that frozen coordinates are not subject to pressure scaling." So, it seems that to avoid spurious contribution to the pressure, I need to exclude interactions between completely frozen atoms. I used the following directives in my .mdp file: energygrps = GR1 GR2 freezegrps = GR1 GR2 freezedim = Y Y Y Y Y Y ; freeze x, y & z directions energygrp_excl = GR1 GR1 GR2 GR2 GR1 GR2 This series of directives, I think, should tell Gromacs to exclude the nonbonded interactions between atoms within GR1, between atoms within GR2, and between atoms in GR1 and in GR2. However, when I run g_energy to extract the (average) pressure (selecting "Pressure" from the menu in g_energy), it turns out that the pressure is the same with or without the energy group exclusion defined by my directive energygrp_excl above; the average pressure in each case is a whopping 6.91498*10^29 bar (and the RMSDs are the same, too). So it seems that the "spurious contribution to the pressure" described in the manual is not actually being removed by my energy exclusions. Can you please help me think what I may be doing wrong, or how I can otheriwse remove the "spurious contribution to the pressure" in the case of freeze groups? Or, is the key sentence in the manual actually "Note that frozen coordinates are not subject to pressure scaling."? What does it mean that frozen coordinates are not subject to pressure scaling? Does this mean that the pressure is not computed for freeze groups? Thank you so very much for your time! I truly appreciate it. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-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
