On 6/12/12 4:13 AM, Satish Kamath wrote:
I've refined the charge distribution.
nr type resnr resid atom cgnr charge- prodrg (NEW) mass
1 OA 1 F09 OAD 1 -0.117 (-0.596) 15.9994
2 H 1 F09 HAD 1 0.027 (+0.469) 1.0080
3 C 1 F09 CAC 1 0.078 (+0.274) 12.0110
4 CR1 1 F09 CAF 1 -0.005 (-0.390) 12.0110
5 HC 1 F09 HAF 1 0.014 (+0.195) 1.0080
6 C 1 F09 CAH 1 -0.014 (+0.104) 12.0110
7 CR1 1 F09 CAI 1 -0.006 (-0.197) 12.0110
8 HC 1 F09 HAI 1 0.014 (+0.140) 1.0080
9 CR1 1 F09 CAK 1 -0.005 (-0.139) 12.0110
10 HC 1 F09 HAK 1 0.014 (+0.139) 1.0080
11 CR1 1 F09 CAL 2 -0.006 (-0.139) 12.0110
12 HC 1 F09 HAL 2 0.014 (+0.139) 1.0080
13 CR1 1 F09 CAJ 2 -0.005 (-0.197) 12.0110
14 HC 1 F09 HAJ 2 0.014 (+0.140) 1.0080
15 C 1 F09 CAG 2 -0.014 (+0.104) 12.0110
16 CR1 1 F09 CAA 2 -0.005 (-0.390) 12.0110
17 HC 1 F09 HAA 2 0.013 (+0.195) 1.0080
18 C 1 F09 CAB 2 0.078 (+0.274) 12.0110
19 OA 1 F09 OAE 2 -0.116 (-0.594) 15.9994
20 H 1 F09 HAE 2 0.027 (+0.469) 1.0080
The ones in the bracket are the new charges applied. These are from the
Automated Topology Builder which does the QM calculations. They seemed more
appropriate as they match with the ones on p-cresol in the paper. I did not
modify the bond parameters from PRODRG as suggested by the paper. The
potential energy has reduced and is arnd 1.5e+04 but is still positive. Can
I get some help with this? Thank you for all the help in advance. :)
Those charges certainly do look better. How long are your simulations? It may
take quite a while for your system to rearrange and equilibrate appropriately.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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