Zuzana Benkova wrote:
Dear GROMACS users,
I have checked the mails in archive which deal with the problem I am
facing but did not find the answer what I do wrong.
I want to compile a PEO chain centered in box of 2900 water molecules.
In my md.mdp the relevant section is as follows
Tcoupl = nose-hoover
tc-grps = PEO SOL
tau_t = 0.1 0.1
ref_t = 50 50
gen_vel = yes
gen_temp = 50 50
I have generated an index file where I have defined the PEO group. The [
SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms.
This matches with the gro file. I tried to prepare a tpr file using
You shouldn't have to do this. By default, each moleculetype is given its own
default index group:
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p
topol.top -o PEO18_2900TIP3P_50K
and got message
Program grompp, VERSION 4.0.3
Source code file: readir.c, line: 1050
Fatal error:
16 atoms are not part of any of the T-Coupling groups
I tried the compilations with 4.0.3 and 4.0.5 versions but the message
was the same.
This is not a version-specific bug, so I'd imagine not. There's something in
your system that is not coupled. Perhaps you've done something wrong in setting
the index groups. Try without an index file (see above comment). If there's
something else in the system, it needs to be accounted for.
-Justin
I would be really thankful for an advice which can move me further.
Thank you in advance.
Zuzana
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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