[gmx-users] problem about distance restraint in REMD simulation

[Mark Abraham]

Hi,

That check is unfortunately a little bit overzealous. I have proposed a fix
for the upcoming 5.1.3 release. If you want to fix your 4.6 version (but
you should anyway not start new work on such old versions of GROMACS) then
you can go to src/gmxlib/disre.c and change

        if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL
||

to

        if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble ||

and recompile and reinstall.

Mark

On Sun, Jun 12, 2016 at 11:59 AM 曾娟 <zengjuan at pkusz.edu.cn> wrote:

> Dear Users:
>
> I have a system with four distance restraints to maintain a
> hydrogen-bonding network in REMD simulation. While when I applied the
> distance restraint, the REMD simulation is only ok when applied single CPU
> for each replica. When I applied more than one CPU for each replica, there
> are error message like this: "Time or ensemble averaged or multiple pair
> distance restraints do not work (yet) with domain decomposition, use
> particle decomposition (mdrun option -pd)". But the "-pd" option can not
> solve the problem. I have also read some archives, but still unknow how to
> solve the problem. Can you give me some advices. Thanks!
> My file added distance restraint is:
> ; distance restraints for r_46_&_N_or_r_50_&_O of Protein in water
> [ distance_restraints ]
> ;   i     j ? label      funct         lo        up1        up2     weight
>   409   467 1     0          1   0.210000   0.390000    0.50000          1
>   421   464 1     1          1   0.210000   0.390000    0.50000          1
>   423   440 1     2          1   0.210000   0.390000    0.50000          1
>   425   447 1     3          1   0.210000   0.390000    0.50000          1
> And my mdp file is :
> cpp            = /usr/bin/cpp
> integrator     = md
> define         = -DPOSRES
> dt              = 0.0025
> nsteps          = 600000000
> constraints     = hbonds
> disre           = simple
> disre-fc        = 1000
> nstxout         = 0
> nstvout         = 0
> nstxtcout       = 600
> xtc_grps        = Protein
> nstlog          = 600
> nstenergy       = 600
> nstlist           = 5
> ns_type           = grid
> rlist             = 0.9
> coulombtype       = PME
> rcoulomb          = 0.9
> vdwtype           = cut-off
> rvdw              = 0.9
> DispCorr          = EnerPres
> Tcoupl              = v-rescale
> tc_grps             =  system
> tau_t               =  0.2
> ref_t               =  290.0
> Pcoupl              = no
> gen_vel             = no
>
>
> Juan
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