Dear all,
I think I found the reason for the deviation after "hunderds of small
runs"...:-): I normally used Dispersion Correction for both the energy
and pressure because in the manual the following is noted:
"...The pressure correction in contrast is very large and can not be
neglected. Although it is in principle possible to
parameterize a force field such that the pressure is close to 1 bar even
without correction, such a method makes
the parameterization dependent on the cut-off and is therefore
undesirable. Please note that it is not consistent to
use the long range correction to the dispersion without using either a
reaction field method or a proper long range
electrostatics method such as Ewald summation or PPPM."
Maybe I got it wrong (and I am still a little bit confused) but because
I used the reaction-field approximation I turned on DispCorr for
Pressure. However, it seems that the Gromos DMSO FF was established in a
way that the correction is "included" in the parameter set which was /
is not clear to me when reading the DMSO paper.
And thank you Berk for the explanation of the Orire parameters.
CU,
Andreas
Berk Hess wrote:
------------------------------------------------------------------------
> Date: Wed, 12 Mar 2008 12:31:12 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs
>
> Hi Berk,
>
> Thanks for replying so quick. I made it rigid in that way that I used
> bonded interactions also for the groups that are not directly connected
> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the
> other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.
>
> Andreas
There could be another issue.
With reaction-field you always introduce integration errors.
With water this leads to a temperature of 305 K when Berendsen coupling
to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.
In Gromos there is/was a problem with inconsistent ways of determining
the temperature. Therefore the effective temperature in the simulation
can be several degrees higher than the one reported in the paper.
What coupling method did you use and what is your real temperature?
Berk.
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