lindahl at stanford.edu
Sat Jul 27 20:29:44 CEST 2002
Nguyen Hoang Phuong wrote:
>I use the program tpbconv to remove the solvent from my tpr file and rerun
>the simulation without solvent. The simualtion is crashed with the error:
>Fatal error: calloc for theta[i] (nelem=-21307068, elsize=8, file pme.c,
>line 699): Cannot allocate memory
>Can anyone tell me what is wrong here? Thanks in advance.
Yes, as it says in the help text for tpbconv (tpbconv -h) you can not
run a simulation with a tpr file
created by removing some of the atoms. It is only useful when you have
written a subset of your system
e.g. to an xtc file, and need a convenient tpr file to analyze this
subset of the system.
Just comment out the solvent line in your topology, run trjconv to
create a gro file with only the protein,
and then grompp to create a new input file. You should probably change
the center-of-mass motion
removal to remove angular motion if you are simulating in vacuuo.
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