[EMAIL PROTECTED] wrote:
Hi all,
I have been trying to simulate peptide (octa alanine). In genbox i have
inserted 40 molecule of guanidium ion & 800 water molecule (by -ci &
maxsol option in gromacs 3.3.3)then again with genbox i added 40
molecules of thiocynate ion & 80 water molecules as above mentioned way.
When i tried to do grompp for energy minimization i was encountered with
many warning listed below though i have included the *.itp files of both
ions in the topology *.top file of peptide.I need some insight about this
so that i can resolve this problem.
I have attached the em.mdp file along with this mail.
This is not the problem, but your T-coupling groups aren't useful. See
http://wiki.gromacs.org/index.php/thermostats
If i will be getting help i'll be thankful for you.
The order of molecules in your .top files [ molecules ] section probably
doesn't match the order of molecules in your structure file. See chapter
5 of the GROMACS manual if you don't understand this.
Mark
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