[gmx-users] Fw:Re:gmx-users Digest, Vol 97, Issue 218

[MD]

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,gmx-users-request at gromacs.org wrote:
>Send gmx-users mailing list submissions to
>	gmx-users at gromacs.org
>
>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
>	gmx-users-request at gromacs.org
>
>You can reach the person managing the list at
>	gmx-users-owner at gromacs.org
>
>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  <ptf1242 at 163.com>
>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: gmx-users at gromacs.org
>Message-ID: <1dc9ba2d.c95b.1379caa467e.Coremail.ptf1242 at 163.com>
>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 <Mark.Abraham at anu.edu.au>
>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 <gmx-users at gromacs.org>
>Message-ID: <4FC5CF81.7000203 at anu.edu.au>
>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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120530/edcf47d8/attachment.html>