[gmx-users] Weird structure after minimization (membrane protein simulation)

Alok alokjain at iitk.ac.in
Sun Feb 3 14:07:05 CET 2008

Dear Mark and Chris,

Thanks a lot for your suggestions which gave me idea to solve the problem.

I have run the minimization again, without the FLEXIBLE water molecules. 
After the minimization, structure looks perfectly ok to me. please have a 
look at the new snapshoot. 

It is just my speculation that because I am using the TIP4P water model, 
which has dummy atom (-1.04 charge), it might be possible that due to this 
water hydrogen's (+0.52 charge) are attracted to the dummy atom of nearby 
water molecules. That's why if I closely observed the structures (after 
minimization using flexible water model) then, some water molecules 
aggregates, and leave some vacuum at other places, that's why structure was 
looking weird. It is just my speculation please correct me if I am missing

I have also checked the bond and angle energy values and when I was using 
the flexible water model it deviate a lot. For bond energy it increases 
8.88556e+04 to 4.10925e+07 and for angle energy 3.60214e+04 to 1.09253e+06 
these energy compensated by short range Coulomb which changes -1.65898e+07 
to -1.71941e+08 .

Without flexible water molecules there is no such huge deviation from the 
original value.Also during the equilibration run I have not observed any 
LINCS warnings. I am hoping my problem is solved now :-)

Thanks again to your valuable suggestions.

Best regards,
Alok Jain

----- Original Message ----- 
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, February 01, 2008 5:04 AM
Subject: Re: [gmx-users] Weird structureafter minimization (membrane 

> alokjain at iitk.ac.in wrote:
>> 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.
> OK
>> 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.
> Is this distribution the only one you have installed? If not, you want to 
> take care that GMXLIB is pointing to the right spot so that you're 
> actually including the .itp files you think you are.
> I realise that make_hole requires some early version of GROMACS, but once 
> it has been run, perhaps you should take its output structure and use a 
> 3.3.x version from there.
>> 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.
> OK, well there goes that idea.
> Mark
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