[gmx-users] pull code bug?
convertino at farmchim.uniba.it
Mon Mar 20 17:59:34 CET 2006
sorry for the long message.
I am simulating the hydrophobic interaction between two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent with all-bonds constraints (LINCS) by GROMACS 3.3 downloaded from GROMACS web-site.
In order to allow them to interact I am using pull code.
My pull.ppa is as follows:
verbose = no
runtype = afm
group_1 = p2 ;protein_2 residues 43-84
reference_group = p1 ; protein_1 residues 1-42
reftype = com_t0
reflag = 1
pulldim = Y Y Y
afm_rate1 = 0.025
afm_k1 = 1000
afm_init1 = 0.0 0.0 0.0
afm_dir1 = 0.0 0.0 0.1
I am giving the following commands:
>grompp -f PME_NPT_fullMD.mdp -c Pull_2_eql.gro -p Pull.top -o Pull_fullMD.tpr -v
>mdrun -s Pull_fullMD.tpr -o Pull_fullMD.trr -c Pull_fullMD.gro -e Pull_fullMD.edr -pi pull.ppa -pn pull.ndx -po -pdo -v > & fullMD.log &
Unfortunately, the calculation does not start and checking the fullMD.log I have returned as follows:
Program mdrun, VERSION 3.3_beta_20050202
Source code file: pullinit.c, line: 215
in the index file2
Halting program mdrun
I think that the file2 means 'file p2' (the group_1 in the Pull.ppa, infact changing that name, also the error change accordingly)
Can anyone help me?
What can I do in order to solve this problem?
Thanks in advance.
Dept. Farmaco Chimico
University of Bari
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