[gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?

[Alok]

Dear Chris,

I have ran the equilibration run till 225ps but water molecule are not ready 
to stay at my desirable place :-( , I mean to say still I am getting uneven 
distribution of water moleculers over lipid head groups. Even after changing 
0 to 4.5e-5.

PS: I have send a personal mail to Mark Abraham, because I have to send a 
picture to explain my problem, which gromacs mailing list does not permit. 
After that he gave me couples of suggetions. I have follow his suggetions 
along with incorporation of your suggetion (0 to 4.5e-5), till now it looks 
like my problem is solved.

Thanks a lot for your valuable comments/suggetions.

Best Regards,
Alok




----- Original Message ----- 
From: <chris.neale at utoronto.ca>
To: <gmx-users at gromacs.org>
Sent: Friday, October 26, 2007 2:33 AM
Subject: [gmx-users] solvate using genbox results in water in thecenterofthe 
bilayer. How to edit pdb file contents in gromacs ?


>> Dear Chris,
>>
>> Thanks a lot your  suggestions.
>>
>> I have started the MD  based on your suggestions. I will tell you as 
>> soon I will get the results.
>
> ok, great.
>
>> PS: Is this is already reported that Gromacs have some problem with ZERO?
>
> No. And I don't believe that gromacs has a problem here. But it is 
> something that you could test. For example... is the z changing at all  in 
> your simulation? I only mentioned anything about it because I have  no 
> personal knowledge that it works correctly with zeroes from my own 
> experience. That of course doesn't make it incorrect :) but I would 
> prefer for you to try using some set of conditions that I do know 
> personally to work correctly.
>
>>
>> Regards,
>> Alok
>
>
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