[gmx-users] TIP4P and cg ?

[David van der Spoel]

On Wed, 18 Feb 2004, Erik Lindahl wrote:

>Hi Weihua,
>
>Water molecules are a bit special since they use "SETTLE" constraints 
>and not normal bonds.
>
>The easiest thing is probably to
>


No, it's all been taken care of in the tip4p.itp file. Just add
define = -DFLEXIBLE
to you mdp file


>1. Copy the tip4p.itp file and make a flextip4p.itp (or something)
>2. Replace the [ settles ] section with bonds - you can use the same 
>parameters as for flexible spc to start with.
>3. Edit the topology to include your modified file when FLEXIBLE is 
>defined.
>
>Cheers,
>
>Erik
>
>On Feb 18, 2004, at 12:57 AM, Weihua Guo wrote:
>
>>
>> Hi gmxusers,
>>
>>  Does anyone have a "flexible" type of tip4p.itp that I can use for
>>  conjugate gradient minimization?
>>
>>  My system is a solvated (TIP4P) peptide in opls force field. Using cg 
>> to
>>  minimize requires the system completely free of constraints. If I use
>>  "define = -DFLEXIBLE" it will point to the flexible spc water, which 
>> has
>>  different number of particles with tip4p and "grompp" won't work.
>>
>>  Will the minimization work fine if I just remove the "exclusions" part
>>  from the tip4p itp file?
>>
>>  Thanks,
>>  Weihua Guo
>>
>>
>> Weihua Guo
>> The University of Chicago
>> 5735 S Ellis Ave
>> Chicago, IL 60637
>>
>>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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