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

[alokjain at iitk.ac.in]

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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