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

[Christopher Neale]

This is essentially what I have done and it worked fine for me. In fact, not being as clever as Mark I simply commented out that entire if/gmx_fatal block of code and use this modified code only in cases where I an not concerned about other side-effects. It is stable for >500 ns/replica.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of 曾娟 <zengjuan at pkusz.edu.cn>
Sent: 12 June 2016 21:39:56
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] problem about distance restraint in REMD simulation

Dear Mark,

Thank you for your replay. It is very usefull for me.

Juan

> -----原始邮件-----
> 发件人: "Mark Abraham" <mark.j.abraham at gmail.com>
> 发送时间: 2016-06-12 22:51:52 (星期日)
> 收件人: gmx-users at gromacs.org
> 抄送:
> 主题: Re: [gmx-users] problem about distance restraint in REMD simulation
>
> 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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