[gmx-users] Polarizative models for water

[Dmitri Dubov]

Dear David,

Thanks for your short but instructive reply. Now I've 
start the simulation with your SW-model and see that it 
runs tenfold slower than analogues simulation with 
non-polarizative TIP4P water cluster.  An energy 
minimization of the shell particle positions is so 
time-consuming, isn't it? How can I minimize the energy 
only at every Nth step?

Sincerely,
Dmitri
-----------------------------------------------------------
On Mon, 28 Apr 2008 10:49:38 +0200
  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Dmitri Dubov wrote:
>> (for David van der Spoel, imho)
>> 
>> Dear David,
>> 
>> I am doing some similations of large water cluster with 
>>tip4p flexible model. I would like to include 
>>polarizability effect in the simulation, but trying it 
>>get twofold problem.
>> 
>> First, I need the input gro-file with dummy and shell 
>>particles. I failed to apply your utility "mkyaw" to my 
>>tip4p-structure file directly, since it remained in final 
>>file virtual sites MW. Then I reduced my tip4 structure 
>>to spc and generated correct gro-file with dummy and 
>>shell and without virtuals MW. But! I see that 
>>coordinates of both dummy and shell particles coincide 
>>with oxygen atoms! Is it acceptable or the result of some 
>>mistake of mine?
>> 
>> I cannot examine this (and it is the second problem), 
>>since I don't understand how topology file should be 
>>generated. I find here the instruction "to use sw.itp 
>>instead of spc.itp". But formal replacement in pdb2gmx 
>>option "-water" is impossible. Should I
>> #include "sw.itp"
>> into top-file manually? Is it enough? Could you give me 
>>more detailed instructions?
>> 
>> And the last question. As I know at least three 
>>polarizative models of water are implemented in GMX. The 
>>sw.itp file with your parametrization is in GROMACS 
>>distributives, the file of parameters for Roux group's 
>>model can be found in gmx-users archive. What about the 
>>third model (I mean the model of Gunsteren group)? Is it 
>>possible to get their parameter file?
>> 
> 
> You can easily make it yourself. Read chapter 5 in the 
>manual and read the paper carefully.
> 
>For mkyaw you should check the extra flags (mkyaw -h).
> 
> You don't need pdb2gmx anywhere for water clusters.
> 
> 
>> Thank you in advance
>> 
>> Sincerely,
>> Dmitri
>> 
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>>http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. 
>>Use the 
>> www interface or send it to 
>>gmx-users-request at gromacs.org.
>> Can't post? Read 
>>http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., 
>Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. 
>Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org 
>  http://folding.bmc.uu.se
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
>http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. 
>Use the www interface or send it to 
>gmx-users-request at gromacs.org.
> Can't post? Read 
>http://www.gromacs.org/mailing_lists/users.php