[gmx-users] Re: NPT and NVT simulations

[Nilesh Dhumal]

I am using opls force field. I have solvent.itp file.
I added follwing line in my solvent.itp file.
[ constraints ]
 opls_997  opls_998   1    0.350000
I am getting the following error

Fatal error:
Syntax error - File solvent.itp, line 13
Last line read:
' [ constraints ]'
Invalid order for directive constraints

Nilesh


On Tue, July 27, 2010 11:29 am, Justin A. Lemkul wrote:
>

> Yes, if you define it in a [ constraints ] directive, and use
> "constraints =
> none" in your .mdp file, so that other bonds will not be converted to
> constraints, but the one you explicitly set in the topology will be used.
>
>
> -Justin
>
>
> Nilesh Dhumal wrote:
>
>> Can I put constraint on selected bond?
>> Nilesh
>>
>>
>> On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote:
>>
>>> 1. Using freezegrps is not generally a good idea to fix a bond
>>> length. Look at the constraints mechenism better. Or just try a bigger
>>> force constant in topology.
>>>
>>> 2. NPT and freezegrps do not interact correctly, since freezegrps
>>> just freezes any changes of atom positions, so they are not rescaled
>>> even if the box size is changed in NPT.
>>>
>>> 3. Anyway, I think you have defined incorrect groups if your atoms of
>>>  interest are still movable. Check a diffusion constant of your
>>> bonded atoms, it should be zero in the case of freezegrps.
>>>
>>> Dr. Vitaly Chaban
>>>
>>>
>>>
>>>
>>>
>>>
>>>> I am trying to freeze a bond (3.5 A) in my system.  I used the
>>>> index file to define group and I added this two lines in my .mdp
>>>> file.
>>>>
>>>> freezegrps         = PA NE freezedim   = Y Y Y Y Y Y
>>>>
>>>> I used g_dist to verify the distance between the freezing atoms.
>>>> During
>>>> the NVT simulation the distace is around 3.449 A and its constant
>>>> though out the simulation. For NPT simulation the distance varies
>>>> from 3.449 to
>>>> 3.1.
>>>> Can you tell why distance changes in NPT not in NVT.
>>>> How can I freeze a bond om NPT simulation?
>>>>
>>>>
>>>>
>>> --
>>> 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
>>>
>>>
>>>
>>>
>>
>>
>
> --
> ========================================
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> ========================================
> --
> 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
>
>
>