[gmx-users] Re: shake vs settle for water

[David van der Spoel]

Rahul Godawat wrote:
> Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time
> step 2 fs...... and OS --- RedHat Enterprise Linux, I hv been using 3.2.1
> for a while apart from that no specific reason for using 3.2.1
> 
> dt                  =  0.002			; time step (ps)
> nsteps              =  100000			; number of steps
> comm_mode           =  Linear
> comm_grps           =  System
> energygrps         =  OW  HW
try removing the line above

> nstcomm             =  10			; reset c.o.m. motion
> nstxout             =  500			; write coords
> nstvout             =  500			; write velocities
> nstlog		    =  500			; print to logfile
> nstenergy           =  500			; print energies
> nstlist             =  10			; update pairlist
> ns_type             =  grid			; pairlist method
> coulombtype         =  PME
> rvdw                =  1.0			; cut-off for vdw
> rcoulomb            =  1.0			; cut-off for coulomb
> rlist               =  1.0			; cut-off for coulomb
> Tcoupl              =  Berendsen 
> tc-grps		    =  System 
> tau_t		    =  0.5   
> ref_t               =  300   
> 
> 
> Thanks
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of gmx-users-request at gromacs.org
> Sent: Wednesday, June 07, 2006 3:35 PM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 26, Issue 32
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> Today's Topics:
> 
>    1. Free volume: Pass and Gromacs (Alessandro Mattozzi)
>    2. Re: Free volume: Pass and Gromacs (David van der Spoel)
>    3. Re: Freezing part of the molecules!!! (Soren Enemark)
>    4. Re: Freezing part of the molecules!!! (David van der Spoel)
>    5. shake vs settle for water (Rahul Godawat)
>    6. diffusivity computations (Debashis Dutta)
>    7. Re: shake vs settle for water (David van der Spoel)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 7 Jun 2006 17:11:03 +0200
> From: "Alessandro Mattozzi" <Alessandro at polymer.kth.se>
> Subject: [gmx-users] Free volume: Pass and Gromacs
> To: <gmx-users at gromacs.org>
> Message-ID:
> 	<B190919A5A0D684E9AC628C8574166521CFFEF at kvaser2.mimer.kth.se>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi all
> I wonder if anybody has been using Pass to measure free volume: I got these
> errors:
>  
> -Error:  Found an odd element (B) on atom #13454.  Hydrogen radius assigned.
> Suggestion: Do I have to remove all the dummies?
> 
> -Segmentation fault
> Suggestion: I use trjconv to get a pdb; is it possible that I am doing some
> mistake in the conversion?
> 
> Thanx
> 
> Alessandro Mattozzi
> M.Phil., Ph.D. student
> Dept. of Fibre and Polymer Technology
> Royal Institute of Technology
> Stockholm, Sweden
> 
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> ------------------------------
> 
> Message: 2
> Date: Wed, 07 Jun 2006 17:14:59 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Free volume: Pass and Gromacs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4486ED73.9020904 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Alessandro Mattozzi wrote:
> 
>>Hi all
>>I wonder if anybody has been using Pass to measure free volume: I got 
>>these errors:
>>
>>-Error:  Found an odd element (B) on atom #13454.  Hydrogen radius
> 
> assigned.
> 
>>Suggestion: Do I have to remove all the dummies?
> 
> Yes.
> 
> make an index file, it will have a suitable group for it.
> 
> 
>>-Segmentation fault
>>Suggestion: I use trjconv to get a pdb; is it possible that I am doing 
>>some mistake in the conversion?
>>
>>Thanx
>>
>>Alessandro Mattozzi
>>M.Phil., Ph.D. student
>>Dept. of Fibre and Polymer Technology
>>Royal Institute of Technology
>>Stockholm, Sweden
>>
>>
>>------------------------------------------------------------------------
>>
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> 
> 


-- 
David.
________________________________________________________________________
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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