[gmx-users] Weird structure after minimization (membrane proteinsimulation

[alokjain at iitk.ac.in]

Sorry again,

I just checked in case of TIP4P water molecules there is separate section 
 [ constraints ] which is used if we do not use FLEXIBLE water. It does
not uses SETTLE algorithm for constraining water molecules (correct me if
I am wrong). Sorry for my previous mail.

Regards,
Alok



> Dear Mark,
>
> Thanks a lot for your reply.
>
> Default was 1.6 angstrom and when I change gradually till 2.5 angstrom
> then
> structure looks similar to original structure.
>
> I have again checked in my top and mdp files for include statement.
>
> I have define = -DFLEXIBLE in my mdp file
>
> in my top file I have included the tip4p.itp file as follow.
> #include "tip4p.itp"
>
> which must open the tip4p.itp file comes with the distribution which has
> following section
>
> #######################################################################
>
> [ moleculetype ]
> ; molname nrexcl
> SOL  2
>
> [ atoms ]
> ; id at type res nr  residu name at name cg nr charge
> #ifdef _FF_OPLS
> 1 opls_115 1 SOL MW1 1      -1.04
> 2 opls_114 1 SOL HW2 1        0.52
> 3 opls_114 1 SOL HW3 1        0.52
> 4 opls_113 1 SOL OW4 1        0
>
>
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j funct length force.c.
> 4 2 1 0.09572 502416.0 0.09572 502416.0
> 4 3 1 0.09572 502416.0 0.09572 502416.0
>
> [ angles ]
> ; i j k funct angle force.c.
> 2 4 3 1 104.52 628.02 104.52 628.02
>
> ########################################################
>
> I have also checked my tpr file using gmxdump and searched for SETTLE
> term, but I did not observe any SETTLE term. it's means my include/define
> statement are working fine and during minimization I am not using SETTLE
> (please correct me if I am wrong).
>
> Actually in my previos mail I have pasted the link of plots
> (http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg )
> which Chris had asked me to plot. These plots give the idea of the number
> of atoms inside the hole created in the membrane and how deep these atoms
> are
> present after imposing the force by using modified version of mdrun
> program,
> which ultimetly validate my procure of mdrun_hole. I want to know my plots
> look fine or not (for me it looks fine !!), but your expert comments will
> give me confidence .
>
> Still I am at the same point, I am not able to resolve my problem :-(
>
> Best regards,
> Alok
>
>
>
>> Alok wrote:
>>> Dear Mark & Chris,
>>>
>>> Thanks a lot for your help.
>>>
>>> As both of you suggested I have increased the tolerence limit of the
>>> bond (using VMD, as described by Chris), after increasing the Dynamic
>>> bond lenth, the structure looks fine.
>>
>> How long did you have to make the O-H bonds before it looked like all of
>>   them were being "made"?
>>
>>> So it means that during
>>> mimimization, position of water hydrogens are moved further to their
>>> ideal limit. So what could be the possible reason for that?
>>
>> A broken water model, so check your .top, and the #include file with the
>> water molecule topology, and pay attention to how the #ifdef mechanism
>> is working in concert with anything in your "define = xxx" .mdp file
>> entry.
>>
>>> Is this the
>>> problem of my initial structure or that of mimimization parameters
>>> (em.mdp)?
>>
>> Likely neither, except inasmuch as "define =" selects which bit of the
>> topology file is being used.
>>
>>> what do you think about my plots from md_run data? Do they look fine or
>>> that could be the root of the problem?
>>
>> Not sure what you mean here.
>>
>> Mark
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