[gmx-users] Problem in mdrun

Alok alokjain at iitk.ac.in
Sun Sep 12 22:52:52 CEST 2004

     Thanks for ur precious advise !
but now i am facing problem in mdrun .
upto grompp all thing are going fine but when i start mdrun i am facing some problem ..
 I was trying to genrate .gro (output which only contain coordinates i.e. dppc128out.gro) and .xtc(dppc128.xtc) file but these file
are not genrating . or there is any other way to genrate a file which contain only coordinates not other outputs(like velocity,energy etc..).
can u give me some advise  again .......
my input for mdrun is as follows (dppc128 is my file name)
mdrun -v -s dppc128 -e dppc128 -o dppc128 -c dppc128out -x dppc128 -g
dppc128 >& dppc128.job &

Thanks !

                              Alok Jain
  ----- Original Message ----- 
  From: Arlan Gonçalves 
  To: gmx-users at gromacs.org 
  Sent: Sunday, September 12, 2004 2:50 AM
  Subject: [gmx-users] Re: Problem in grompp

  Hello Alok,
          Try to follow this order, before the energy minimization, where ache is the name of your pdb file:

  pdb2gmx -f ache.pdb -o ache.gro -p ache.top

  editconf -bt cubic -f ache.gro -o ache.gro -c -d 0.65

  genbox -cp ache.gro -cs spc216.gro -o ache_st.gro -p ache.top

  make_ndx -f ache

                        Arlan da Silva Gonçalves


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