[gmx-users] NPT simulation for mutation study

[David van der Spoel]

On 2012-04-16 17:23, Shyno Mathew wrote:
> Dear Gromcas users,
> I am doing some mutation study, NPT simulations. Initially I was using a
> generic .mdp file I got from my advisor and I was able to run the
> systems for ~50ns with out any issues.
> But then I spend time reading about gromacs and created a .mdp file.
> However, with my .mdp file the runs are crashing with error:
> Fatal error:
> The X-size of the box (4.500406) times the triclinic skew factor
> (1.000000) is smaller than the number of DD cells (5) times the smallest
> allowed cell size (0.900000)

use isotropic pressure scaling.
if you make mutations, take care to use the same number of water 
molecules and ions, such that you can compare the energies of the systems.

> I understand I can try particle decomposition for this system, but
> before I want to make sure there is no error in my .mdp file.
> When I load the trajectory in the vmd, I can see the box is getting
> compressed too much. The contents of the current .mdp file are shown below.
> This .mdp file varies from my advisor's for few parameters which I have
> shown at the end.
>
> contents of my .mdp file:
> title                    = Yo
> cpp                      = /usr/bin/cpp
> include                  =
> define                   =
> integrator               = sd
> tinit                    = 0.0
> dt                       = 0.002
> nsteps                   = 50000000
> nstxout                  = 1000000
> nstvout                  = 1000000
> nstfout                  = 1000000
> nstlog                   = 10000
> nstenergy                = 10000
> nstxtcout                = 10000
> xtc_precision            = 1000
> xtc_grps                 =
> energygrps               =
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 0.9
> domain-decomposition     = no
> coulombtype              = PME
> fourierspacing           = 0.12
> pme_order                = 4
> ewald_rtol               = 1e-05
> optimize_fft             = no
> epsilon_surface          = 0
> ewald_geometry           = 3d
> rcoulomb                 = 0.9
> vdwtype                  = Cut-off
> rvdw                     = 0.9
> epsilon_r                = 1
> DispCorr                 = EnerPres
> ; with sd as integrator tcoupl is ignored
> tc-grps                  = system
> ; good choice for zeta is 0.5 1/s
> tau_t                    = 2.0
> ref_t                    = 310
> pcoupl                   = berendsen
> pcoupltype               = anisotropic
> nstpcouple               = -1
> tau_p                    = 1.0
> compressibility          = 4.6e-5 4.6e-5 4.6e-5 0 0 0
> ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0
> annealing                = no
> ;annealing_npoints       = 3
> ;annealing_time          = 0
> gen_vel                  = no
> gen_temp                 = 310
> gen_seed                 = 173529
> constraints              = all-bonds
> constraint_algorithm     = LINCS
> continuation             = no
> lincs_order              = 4
> lincs_iter               = 1
> lincs_warnangle          = 30
> morse                    = no
> disre                    = no
> disre_weighting          = equal
> disre_mixed              = no
> disre_fc                 = 1000
> disre_tau                = 10
> nstdisreout              = 1000
>
> Parameters that are different in my advisor's file:
> DispCorr                 = Ener
> tau_t                    = 0.20
> compressibility          = 5e-6  5e-6  5e-6  0 0 0
> gen_vel                  = yes
> gen_temp                 = 1
> gen_seed                 = 473529
>
> I thought when using vdw cutoff, it is recommended to use dispersion
> corrections for both pressure and energy. Also can some explain the
> reason behind this?
> For tau_t, I used 2 as it is the recommended value for sd integrator in
> the manual. Also gen_vel has to be no for sd integrator, correct?
> Any help will be appreciated!
>
> Thanks in advance,
> Shyno
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se