[gmx-users] Basic Query

[priyanka srivastava]

Dear Prof. Spoel, 
  
  Many thanks for your reply.
  
  Since the fourier_n* values are associated with the grid sizing, will  these values affect my results drastically? do you suggest resubmitting  these runs?
  
  regards,
  Pri...
  

David van der Spoel <spoel at xray.bmc.uu.se> wrote:  priyanka srivastava wrote:
> Hie,
> 
> Many thanks for your reply.
> 
> Yes I have used semi-isotropic coupling.
> 
> Another doubt is why only a value of 4.5e-5?
> 
> I have used PME and have mentioned rcoulomb in the
> .mdp file too, which as is pointed out by you, has no
> meaning!! But does this mean that my mdp file is
> wrong? Because if PME does not use rcoulomb it shud
> simply ignore the value.
> Actually I do not want to use twin range cutoff. So, I
> have given rvdw = rlist. Is this alright?
> Portion of my mdp file looks like this:
> 
> ; Electrostatics
> coulombtype             =  PME
> fourier_nx              =  6.4
> fourier_ny              =  5.0
> fourier_nz              =  8.1
these numbers should be integers


> pme_order               =  4
> rcoulomb                =  1.5
> rvdw                    =  1.5
> 
> Also since I have not specified "vdwtype" in the mdp
> file, so it automatically takes Cut-off.
> 
> regards,
> Pri...
> 
> 
> --- Martin H�fling  wrote:
> 
>> Am Mittwoch, 20. Juni 2007 schrieb priyanka
>> srivastava:
>>
>>> I am currently involved in doing a lipid-peptide
>>> simulation under NPAT conditions. The way I have
>>> applied NPAT condition is as follows:
>>>
>>> ref_p                   =  0 1
>>> compressibility         =  0.0 4.5e-5
>> with semiisotropic?
>>
>>> Although while performing analysis it shows that
>> the x
>>> and y dimensions are constant but still I am not
>> sure
>>> about the way I have applied NPAT. Could somone
>> please
>>> tell me the basis behind it?
>> If i am remembering correctly, this is what above
>> values should do:
>>
>> first dimension is x-y second one is the z
>> direction. Reference pressure is 1 
>> for both (obviously makes sense) whereas
>> compressibility set to 0 for x-y 
>> plane prevents box changes in x and y direction. So
>> only z-direction remains 
>> for adjusting pressure.
>>
>>> Another thing is I have used vdwtype: cutoff.
>>> But my intention is not to use the twin range
>> cutoff
>>> at all!! In my case rlist = rcoulomb = rvdw, i.e.
>> all
>>> three are same!! Is this alright? (the coulombtype
>>>         =  PME)
>> Sorry, didn't get that part of your question. Can
>> you post relevant parts of 
>> your mdp and specify it further? Chapter 7 says that
>> parameters for PME are 
>> fourierspacing and pme_order, rcoulomb should not be
>> used then.
>>
>> Cheers
>>  Martin
>> _______________________________________________
>> 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
>>
> 
> 
> 
>        
> ____________________________________________________________________________________
> Pinpoint customers who are looking for what you sell. 
> http://searchmarketing.yahoo.com/
> _______________________________________________
> 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.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://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


       
---------------------------------
Get the free Yahoo! toolbar and rest assured with the added security of spyware protection. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070620/fddd9237/attachment.html>