[AMBER] Water models ?

From: xuemeiwang1103 <xuemeiwang1103.163.com>
Date: Thu, 1 Apr 2010 21:01:05 +0800 (CST)

Hi :
    Thanks a lot for Case and Carlos's detailed suggestions,I have solved the disulfide bonds problem successfully.But now I am puzzeld by another problem .I used the TIP3 water model as my explict water model (SolvateBox TIP3PBOX) ,I found that the water box is no longer a rectangular box when I have done the MD,it looks like a ball,some water molecules even run far away from the center,Is this phenomenon normal(the structure of the protein seems ok)? Is it better to use the "solvateoct" or other water models to aviod this ?Your comments are highly appreciate!
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Received on Thu Apr 01 2010 - 06:30:03 PDT
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