[gmx-users] normal mode analysis

hj zou hjzou at iris3.simm.ac.cn
Mon Nov 29 09:19:46 CET 2004

Dear Nguyen Hoang Phuong ,
      I run into some problems while I use the following nm.mdp file  as recommended by you to do normal mode analysis in GROMACS .
	  when I  use "grompp_d -f nm -p pr -c pr -o pr_nm  -np 4" to prepare tpr file , the following errors are displayed on the screen:
   Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
WARNING 1 [file nm.mdp, line unknown]:
  Can only use nstype=Simple with pbc=no, setting nstype to Simple

ERROR: rcoulomb must be >= rlist
ERROR: rvdw must be >= rlist
ERROR: With vdwtype = Shift rvdw_switch must be < rvdw
WARNING 2 [file nm.mdp, line unknown]:
  rvdw should be 0.1 to 0.3 nm larger than rvdw_switch to account for
  diffusion and the size of charge groups
calling /lib/cpp...
processing topology...
Generated 1125 of the 1326 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
WARNING 3 [file "pr.top", line 36]:
  System has non-zero total charge: 1.000000e-00

processing coordinates...
double-checking input for internal consistency...
There were 3 warnings
Fatal error: There were 3 errors

    Can you tell me how to solve this problem ?
   Any suggestions will be highly appreciated.

the following are the nm.mdp file:
title                    = fabp
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = nm
emtol                    = 0.000001
emstep                   = 0.000001
nstcgsteep               = 1000
nsteps                   = 500000
nstxout                  = 50
xtc_grps                 = Protein
energygrps               = Protein
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.
vdwtype                  = Shift
coulombtype              = Cut-off
rcoulomb                 = 0.
rvdw                     = 0.
pbc                      = no

   Best regard,

Hanjun Zou 
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Drug Discovery and Design Center
Shanghai Institute of Meteria Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel:   +86-21-50806600-1201
E-mail: hjzou at mail.shcnc.ac.cn


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