[gmx-users] Model of water

[Justin Lemkul]

On 10/6/12 11:52 AM, Shima Arasteh wrote:
>
>
> The total atom of popc-solv.gro is 74672
> grep HW gives me 48698

Assuming you meant to type 48696 like you reported before, this means there are 
24348 water molecules, since there are two HW atoms per water (HW1 and HW2).  If 
you grep for OW (since it is unique to each water molecule), you can confirm the 
count.

> grep P gives me 1628
>

I already said this grep was insufficiently precise and thus it is not possible 
to connect this information with the topology.

> Section of moleculetypes in top file is as
>   [ molecules ]
>   Compound        #mols
>   POPC              238
>   SOL             24348
>
> I am confused! Am I need to change the number of gro or top file? Actually I can't make connection between gro and top, so the coordinate doesn't match topology yet!!
>

You need to make the topology agree with the coordinate file.  Do not make 
manual adjustments to the .gro file.  Sometimes it's better to start over and be 
more careful.  A mismatch between coordinates and topology always boils down to 
errors in bookkeeping.

-Justin

> Please help me :(
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> To: Justin Lemkul <jalemkul at vt.edu>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Saturday, October 6, 2012 6:22 PM
> Subject: Re: [gmx-users] Model of water
>
>
> # grep -c P popc-solv.gro
> 1628
>
> What should I do with this number?
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> Cc:
> Sent: Saturday, October 6, 2012 6:17 PM
> Subject: Re: [gmx-users] Model of water
>
>
>
> On 10/6/12 10:45 AM, Shima Arasteh wrote:
>> Yes, the system is only POPC and water.
>>
>>
>
> Then it should be very easy to count how many molecules are in the system using
> grep.  Your topology specifies a lot more atoms than the coordinate file has.
> The number of water molecules appears right, which leaves only the number of
> POPC as the problem.
>
> -Justin
>
>>
>>
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
>> Cc:
>> Sent: Saturday, October 6, 2012 6:07 PM
>> Subject: Re: [gmx-users] Model of water
>>
>>
>>
>> On 10/6/12 10:32 AM, Shima Arasteh wrote:
>>> OK.
>>> I did as follow as I described, but there is an error:
>>> 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic
>>> 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top
>>>
>>> Then added #include "charmm36.ff/tip3p.itp" to topol.top
>>>
>>> 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr
>>> Fatal error:
>>> number of coordinates in coordinate file (popc-solv.gro, 74672)
>>>                   does not match topology (topol.top, 104936)
>>> I checked the water molecules of popc-solv.gro by grep command ;
>>>
>>> # grep -c HW popc-solv.gro
>>> 48696
>>>
>>>
>>> [ molecules ]
>>> ; Compound        #mols
>>> POPC              238
>>> SOL             24348
>>>
>>>
>>>
>>> What is the problem? would you please help me? I think the SOL molecule are counted twice!!
>>>
>>
>> You're off by a huge amount of atoms, so something is very wrong.  The water
>> molecules do not appear to be the problem.  The number of HW/2 is equal to the
>> number of SOL molecules.  Is the system only POPC in water?  No protein or any
>> other components?
>>
>> -Justin
>>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================