[gmx-users] why the gas ethanol system has positive potential?
tsjerkw at gmail.com
Thu Oct 30 09:40:00 CET 2014
For a single configuration of ethanol, you can do the calculations on a
piece of paper and see if you're doing better than Gromacs.
On Thu, Oct 30, 2014 at 8:27 AM, David van der Spoel <spoel at xray.bmc.uu.se>
> On 2014-10-30 07:27, weiduo zhu wrote:
>> Dear sir,
>> I’m trying to simulate a ethanol gas system, only one ethanol
>> molecule in 10*10*10nm box. but when I analysis the energy, it shows
>> that potential is positive, and the Coul.recip term is very positive
>> throughout the entire run. I think the long range electrostatics
>> (calculated with cutoff) is not okay. But when I simulate liquid
>> ethanol, the potential is okay. I don’t know why this would happen. I
>> need your help, thank you!
>> nstlist = 0
>> ns_type = simple
>> pbc = no
>> rlist = 0
>> coulombtype = cutoff
>> rcoulomb-switch = 0
>> rcoulomb = 0
>> vdw-type = cutoff
>> rvdw-switch = 0
>> rvdw = 0
>> Weiduo Zhu
>> Please post this kind of questions on the mailing list. A positive
> potential is normal, the only thing that matters is the difference in
> energy between gas phase and condensed phase.
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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Tsjerk A. Wassenaar, Ph.D.
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