[gmx-users] TIP4P and cg ?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Feb 18 11:04:03 CET 2004
On Wed, 18 Feb 2004, Erik Lindahl wrote:
>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
>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
>> minimize requires the system completely free of constraints. If I use
>> "define = -DFLEXIBLE" it will point to the flexible spc water, which
>> 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?
>> Weihua Guo
>> Weihua Guo
>> The University of Chicago
>> 5735 S Ellis Ave
>> Chicago, IL 60637
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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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