[gmx-users] Again 1-4 interaction

[David van der Spoel]

On Fri, 7 Dec 2001, Dmitry Kovalsky wrote:

>Hi all
>I have tried to simulate a protein with restraints and get 1-4
>interaction warning. After this when I have read log file I found:
><<<<<<<<<<<<<<<<<
>Going to determine what solvent types we have.
>There are 11573 molecules, 12405 charge groups and 36610 atoms
>There are 0 optimized solvent molecules on node 0
>There are 11571 optimized water molecules on node 0
>>>>>>>>>>>>>>>>>>
>So, during optimization solvent procedure 2 water molecules loss
>occured? Where is a bug, or what I made wrong?
This is not the case, you have 11573 molecules of which 11571 are water,
1 is protein and the other something else..

Regarding the real problem (1-4 warning): did you do proper minimization?
Does the position restraint file match the starting coordinates, such that
you are not pulling the protein away through the solvent. That could lead
to large forces, and hence to this ind of problem. Are your cut=offs long
enough?

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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