David van der Spoel
spoel at xray.bmc.uu.se
Thu May 4 22:04:42 CEST 2006
Marcelo A. Carignano wrote:
> Cutoff I set at 3.00 nm
> The distance between the two molecules is about 0.1 nm.
> The box is a cube of 20 nm
> A bug perhaps?
Could be, please submit a bugzilla.
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of David van der Spoel
> Sent: Thursday, May 04, 2006 3:21 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] cgnr
> Marcelo A. Carignano wrote:
>> Thank you David, but there is no such a term in this case:
> I see, make the cut-off larger. mdrun uses charge group based cutoff
> (see chap 4) and you are probably missing some interactions in the
> second case.
>> (deleted lines)
>> Select the terms you want from the following list
>> LJ-(SR) Coulomb-(SR) Potential Kinetic-En. Total-Energy
>> Temperature Pressure-(bar) Vir-XX Vir-XY Vir-XZ
>> Vir-YX Vir-YY Vir-YZ Vir-ZX Vir-ZY
>> Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) Pres-YX-(bar)
>> Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) Pres-ZY-(bar) Pres-ZZ-(bar)
>> #Surf*SurfTen Mu-X Mu-Y Mu-Z T-rest
>> Any other suggestion?
>> Thank you,
>> Marcelo A. Carignano wrote:
>>> Dear all:
>>> I'm running a test case defining all the interaction parameters in the
>>> topol.top file. My system consist of two NH3 molecules.
>>> Every thing goes well except for the role played by the "cgnr" values:
>>> Depending on how I assign these numbers the calculated Coulombic
>>> interaction changes. If I put the four atoms in the same group, the
>>> energy is not correct. If I put the four atoms in four different chnr's,
>>> the Coulombic interactions are OK:
>> David wrote:
>> check the 14 energy.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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