|
|||||||||||||||||||||||||||||||||
AMBER Archive (2000)Subject: Acetonitrile
From: Jose Ramon Blas (jramon_at_sgbq.bq.ub.es)
Hi,
1)minor problem. XLEAP complains about the sp0 nature of the main atoms(this has been solved by adding some dummy atoms by PREP and reloading). This is a detail.
2)Major problem. When running a SHAKE MD of this system, the Temperature increases and the simulations fails due to a SHAKE error. I have tried to perform SHAKE only on the H-atoms (ntc=2) with the same result. Even removing SHAKE (nstep=0.0005) I find
QUESTION: Is there any way of building an acetonitrile with only 3 atoms with Xleap and then impose distance constraints fully respected during the MD simulation?
Tank you very very much in advance,
Blas
P.D. I'm using AMBER5 and the parameters are OK.
-- J.R. Blas
| |||||||||||||||||||||||||||||||||
|