Dear Gmx Users,
I am trying to run a QM-MM optimization using ORCA and Gromacs 5.1.2
version. I complied gromacs 5.1.2 with ORCA as QM-MM program. Here's the
output of CMakeCache.txt file for QM package:
//QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess,
// orca
Thank you Justin, SI in ffnonbonded.itp is correct.
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On 5/2/16 12:58 PM, zeineb SI CHAIB wrote:
Dear gmx users,
I'm working on simulating a protein with two cofactors (hem and
tetrahydrofolat) and its substrate. I'm in the first stage; generating
topology. I choose CHARMM27 as a force field and I'm little bit confused on how
to generate
Dear gmx users,
I'm working on simulating a protein with two cofactors (hem and
tetrahydrofolat) and its substrate. I'm in the first stage; generating
topology. I choose CHARMM27 as a force field and I'm little bit confused on how
to generate tetrahydrofolate's topology.
I tried the
On 5/2/16 4:53 AM, Ming Tang wrote:
Dear list,
I want to add parameters for silicon in oplsaa.ff
In .rtp I added:
[ SI ]
[ atoms ]
SI opls_966 4.000 0
In .atp I added:
opls_966 28.08000 ; Si
In ffnonbonded.itp I added:
opls_966 Si4+ 1428.08000
Dear gmx-users,
I wanted to calculate the diffusion coefficient of lithium ions is a
solution. I tried using the gmx msd routine first with the options -nomw
and -mol. I want to know if -nomw should be used or not if I want to
compare my results with experiments. Anyway The result I obtained from
Dear gmx users,
I'm working on simulating a protein with two cofactors (hem and
tetrahydrofolat) and its substrate. I'm in the first stage; generating
topology. I choose CHARMM27 as a force field and I'm little bit confused on how
to generate tetrahydrofolate's topology.
I tried the online
Dear all,
Thank your for your answers.
@ Justin,
Actually I was hesitating between CHARMM and Amber force fields, I hadn't
enough informations from my tutors. Finally I'm going with CHARMM 27, it is the
most convenient in my case.
Thank you again for your orientation.
Zeineb.
Dear list,
I want to add parameters for silicon in oplsaa.ff
In .rtp I added:
[ SI ]
[ atoms ]
SI opls_966 4.000 0
In .atp I added:
opls_966 28.08000 ; Si
In ffnonbonded.itp I added:
opls_966 Si4+ 1428.08000 4.000 A4.43500e-01 3.98000e-01
