[gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?
alokjain at iitk.ac.in
Fri Oct 26 08:45:59 CEST 2007
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.
----- 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.
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