From: Alexandra Patriksson <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
Subject: [gmx-users] fep calculation of L-Asn - D-Asn transition
Date: Wed, 24 May 2006 11:11:38 +0200
Dear all,
I'm trying to do a fep calculation of the L to D transition of a amino acid
in a small peptide. We have done some changes to the dihedrals and the
charges in the topology file (see below), but still we get dH/dlambda
values that are far too large. Does anyone have an idea what could possibly
be wrong? Have we forgotten something that should have been taken into
account?
Our changes in the toplogy file going from L -> 0 :
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
7 opls_293B 1 ASN CA 2 0.25 13.019
opls_293B 0 13.019 ; qtot 0.94
8 opls_140 1 ASN HA 2 0.06 0
opls_140 0 0 ; qtot 1
9 opls_136 1 ASN CB 3 -0.12 14.027
opls_136 0 14.027 ; qtot 0.88
10 opls_140 1 ASN HB1 3 0.06 0
opls_140 0 0 ; qtot 0.94
11 opls_140 1 ASN HB2 3 0.06 0
opls_140 0 0 ; qtot 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
7 17 3 8 2 35 0 0
200
7 17 3 9 2 -35 0 0
200
Our changes in the toplogy file going from 0 -> D :
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
7 opls_293B 1 ASN CA 2 0 13.019
opls_293B 0.25 13.019 ; qtot 0.94
8 opls_140 1 ASN HA 2 0 0
opls_140 0.06 0 ; qtot 1
9 opls_136 1 ASN CB 3 0 14.027
opls_136 -0.12 14.027 ; qtot 0.88
10 opls_140 1 ASN HB1 3 0 0
opls_140 0.06 0 ; qtot 0.94
11 opls_140 1 ASN HB2 3 0 0
opls_140 0.06 0 ; qtot 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
7 17 3 8 2 0 200 -35
0
7 17 3 9 2 0 200 35
0
I don't understand why you turned off the charges.
Charge interactions are excluded anyhow for 1-3 interactions.
The problem might be that just turning of the impropers
does not have much effect, as the transition is blocked
by the angle potentials.
I would guess the D-L conversion would happen in one jump
when the improper potential is high enough to overcome
the barrier caused by the angle potentials. This would result
in a large hysteresis.
Turning of the angles (instead of the charges) might help.
Berk.
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