Yes, i try to get a surface tension of 69 dyn, but i can only get 65 at present. Yes, i tried some arbitrary choices. I do not know what is the correct .mdp for me to get a surface tension of 69. May be for this version, it does not include this function Thanks for your kind message. But i still does not how to figure it out.
At 2012-05-30 15:43:36,[email protected] wrote: >Send gmx-users mailing list submissions to > [email protected] > >To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > [email protected] > >You can reach the person managing the list at > [email protected] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-users digest..." > > >Today's Topics: > > 1. can Gromacs 4.5 use VDW long range correction? IN the > mannual, In this version, GROMACS always uses a cut-off radius > for the Lennard-Jones interactions (MD) > 2. Re: can Gromacs 4.5 use VDW long range correction? IN the > mannual, In this version, GROMACS always uses a cut-off radius > for the Lennard-Jones interactions (Mark Abraham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 30 May 2012 15:33:53 +0800 (CST) >From: MD <[email protected]> >Subject: [gmx-users] can Gromacs 4.5 use VDW long range correction? IN > the mannual, In this version, GROMACS always uses a cut-off radius for > the Lennard-Jones interactions >To: [email protected] >Message-ID: <[email protected]> >Content-Type: text/plain; charset="gbk" > >Hi All, > >I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm >for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp >i used are as follow, I really need to know how to get a surface tension of >69.5 dyn for TIP4P/2005 water model. Becasue my surpervisor is so picky, >everything should be perfacet, and i feel really tired by his way. Any comment >will be greatly appreciated, > >The main parameter is > > >coulombtype = PME > >rcoulomb-switch = 0 > >rcoulomb = 1.4 > >; Dielectric constant (DC) for cut-off or DC of reaction field > >epsilon-r = 1 > >; Method for doing Van der Waals > >vdw-type = Cut-off > >; cut-off lengths > >rvdw-switch = 0 > >rvdw = 3.8 > >; Apply long range dispersion corrections for Energy and Pressure > >DispCorr = EnerPres > >; Extension of the potential lookup tables beyond the cut-off > >table-extension = 1 > >; Spacing for the PME/PPPM FFT grid > >fourierspacing = 0.12 > > > >Message: 2 >Date: Wed, 30 May 2012 17:42:57 +1000 >From: Mark Abraham <[email protected]> >Subject: Re: [gmx-users] can Gromacs 4.5 use VDW long range > correction? IN the mannual, In this version, GROMACS always uses a > cut-off radius for the Lennard-Jones interactions >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[email protected]> >Content-Type: text/plain; charset="iso-8859-1" > >On 30/05/2012 5:33 PM, MD wrote: >> Hi All, >> I have to use the long range correction for VDW, in fact i used >> cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we >> can get 65 dyn. The .mdp i used are as follow, I really need to know >> how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. > >By finding the method that was used then and attempting to replicate it? > >> Becasue my surpervisor is so picky, everything should be perfacet, and >> i feel really tired by his way. Any comment will be greatly appreciated, > >A certain degree of pickiness is essential. You're apparently trying to >replicate a result by making some arbitrary choices. Don't. > >This .mdp file generates velocities, thus did not start in an >equilibrium ensemble. However you measured your surface tension needs to >exclude the equilibration time. > >Mark
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