[gmx-users] SHAKE and LINCS

[Mark Abraham]

Justin A. Lemkul wrote:
> 
> 
> Ricardo O. S. Soares wrote:
>> Hello everyone,
>>
>> which one is used by default in case I do not provide any of them in 
>> the mdp file for molecular dynamics?
>>
> 
> You'll have to define "any of them," because if you do not specify the 
> "constraints" keyword in the .mdp file, then no constraints are used.

Caveat: 7.3.18 of manual specifies

constraints: none
No constraints except for those defined explicitly in the topology...

For example, water models are likely to be using SETTLE, etc.

I believe Justin's statement is accurate with respect to molecules whose 
[moleculetype] does not specify [constraints] or [settles], which are 
most "user-defined" ones.

Mark

> If you are indeed specifying some sort of constraints, LINCS is probably 
> default.  You can see for yourself in the mdout.mdp file.
> 
> -Justin
> 
>> Thanks!
>>  
>>
>>
>> ---
>>
>>  
>>
>> Ricardo O. S. Soares , MsC.
>> Group of Biological Physics - Department of Physics & Chemistry
>> Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of 
>> São Paulo.
>> Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo,  Brazil.
>> Phone: +55 16 36024840.
>>
>>
>> ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br
>>
>>  
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>> Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 
>> <http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/> 
>> - Celebridades 
>> <http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/> 
>> - Música 
>> <http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/> 
>> - Esportes 
>> <http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/> 
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.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
>