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

[alokjain at iitk.ac.in]

Dear Mark, & Chris,

Thanks for your useful suggestions.

Yes Mark define = -DFLEXIBLE is the only difference in both the cases.

Actually in my previous post I have pasted only small section of tip4p.itp
file,(sorry if it created unnecessary confusions/doubt). This time I am
pasting full tip4p.itp file. As you expected, it has more #ifdef statements.

I have not modified this file. this is the original file and comes with the
gromacs-3.2.1 distribution. I have cross checked it with the clean
distribution.

I have also compared the order of TIP4P atoms in my structure file
(gro/pdb) and the same is pasted below as TIP4P.itp file. Order is same in
both the
files.

TIP4P.itp File
##################

;
; Note the strange order of atoms to make it faster in gromacs.
;
[ 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
#else
#ifdef _FF_GROMOS96
1       IW              1       SOL     MW1     1      -1.04    0.0
2       H               1       SOL     HW2     1       0.52    1.008
3       H               1       SOL     HW3     1       0.52    1.008
4       OWT4            1       SOL     OW4     1       0       15.9994
#else
1       IW              1       SOL     MW1     1      -1.04
2       HW              1       SOL     HW2     1       0.52
3       HW              1       SOL     HW3     1       0.52
4       OWT4            1       SOL     OW4     1       0
#endif
#endif

#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

#else
[ constraints ]
; i     funct   doh     dhh
4       2       1       0.09572
4       3       1       0.09572
3       2       1       0.15139

[ exclusions ]
1       2       3       4
2       1       3       4
3       1       2       4
4       1       2       3
#endif

; The position of the dummy is computed as follows:
;
;               O
;
;               D
;
;       H               H
;
; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
;         0.015 nm      / [ cos (52.26 deg)     * 0.09572 nm    ]

; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[ dummies3 ]
; Dummy from                    funct   a               b
1       4       2       3       1       0.128012065     0.128012065




Best regards,
Alok Jain





> alokjain at iitk.ac.in wrote:
>> 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
>
> Good, that's a material difference that you can use to find where the
> problem occurs, since this is only present in your EM, not your
> simulation.
>
>> 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
>
> This bears little resemblance to a tip4p.itp file I have in a 3.3.1
> distribution I had lying around.
>
>> #######################################################################
>>
>> [ 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
>
> There should be more #ifdef regions here for various force fields, and
> the atom order is changed from my file. I think this might introduce a
> problem if the atom order in your water molecules in your structure file
> differs, but I'm guessing here.
>
>> #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
>
> These are well-formed, given the above, but if you've given the whole
> tip4p.itp file then there are missing #endifs such that it isn't working
> properly.
>
>> [ angles ]
>> ; i j k funct angle force.c.
>> 2 4 3 1 104.52 628.02 104.52 628.02
>
> Likewise.
>
>> ########################################################
>
> I'd start by finding out where you got this tip4p.itp file, and probably
> hitting someone over the back of the head for messing around
> unnecessarily with it. Or, if it was necessary to change it for some
> purpose, hitting them over the back of the head for letting you have a
> copy of this file, not a normal one :-)
>
> Then, I'd get a clean distribution, start from the beginning, check the
> tip4p.itp file and see how it goes.
>
> Mark
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