[gmx-users] Extending a run for different number of nodes

DimitryASuplatov genesup at gmail.com
Mon Sep 15 10:09:15 CEST 2008

I am sorry to ask this again but I guess that nobody was reading mail on

I have completed a 10ns run. Now I want to extend it to 20ns. The
problem is that the initial tpr was compiled for 8 processors and now
I have only 4 cores.
What I tried to do is used tpbconv to make a 10ns extended tpr, then
used an exactly the same mdp file to grompp it all together with -np 4
to a new tpr file.
The problem is that at the beginning of the trajectory the structure
is undergoing a structural change with 0.12 nm from the initial
structure. That means that the structure is actually relaxing and that
is not something I want to see.
I have used this in my mdp

;------------ VELOCITY INITIATION -----------------------
gen-vel                  = no
gen-temp                 = 300

That means that no velocities were generated and I expect to see no
relaxation but the continuation of my run.

What am I doing wrong? How to extend a run without relaxation.
Thank you. I appreciate any help.

My mdp file is the following.
;-------------PREPROCESSING OPTIONS------------
title                       = PR "1KLC FREE"; my title
cpp                         =  cpp; my C prepocessor (whereIsIt)
include                     = ; dir to include in my topology file
define                      = ;

;-------------RUN CONTROL---------------------
integrator        = md;

;--------------OUTPUT CONTROL------------------
;TRR outpur
nstxout    = 10000
nstvout    = 10000
nstfout    = 0

;LOG and EDR output
nstlog     = 10000
nstenergy  = 10000

;XTC output
nstxtcout  = 1000
xtc-precision   =  1000

;-------------START TIME & TIMESTEP-----------
tinit               =    ; [ps] starting time for your run (only makes
sense for md, sd, bd integator)
dt                  =   0.005 ; [ps] time step for integration (--"--)
nsteps              =   1600000 ; (0) maximum number of steps to
comm-mode           =         ; Linear(Remove center of mass
translation)/Annular(Remove center of mass
;translation and rotation)/No(no restriction)
nstcomm             =  1

;-------------NEIGHBOR SEACHING---------------

nstlist                                       = 5; frequency o update
neighbor list
ns_type                                       = grid; make a gid in
the box and check only
;neighboring grid cell when constructing a new neighbor list
rlist                                         = 1.0; cut-off distance
for the short-range neighbor list

coulombtype              = Reaction-field  ; reaction field with
coulomb cut-off rcoulomb
; where rcoulomb>rlist. The dielectric constant beyond the cut-off is
rcoulomb                                      = 1.5 ;distance for the
coulomb cut-off
epsilon_rf                                     = 80;dielectric constant
epsilon_r                                       = 1;

vdwtype                                       = cut-off; twin-range
cut-off`s with neighbor list cut-off rlist
;and VdW cut-off rvdw, where rvdw>rlist
rvdw                                          = 1.0 ; distance for for
the LJ or Buckingam cut-off

;-------------ENERGY MINIMIZATION-------------
emtol                = 200 (kJ/mol*nm); minimisation is converged when
the maximum force is smaller then this value
emstep               = 0.01; initial step size

;-------------TEMTERAURE CONTROL--------------
tcoupl                   = berendsen
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 300

;--------- PRESSURE CONTROL---------------------
Pcoupl                   = no
Pcoupltype               = Isotropic
tau-p                    = 1
ref_p                    = 1
compressibility          = 4.5E-5

;------------ VELOCITY INITIATION -----------------------
gen-vel                  = no
gen-temp                 = 300

;------------- BONDS -----------------------
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = yes
Shake-SOR                = no
shake-tol                = 0.0001
lincs-order              = 8
lincs-warnangle          = 30
lincs-iter               = 8
morse                    = no

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