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<P><FONT SIZE=2>Thanks, I use ffamber_99.<BR>
<BR>
R. Q.<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org ´ú±í Mark Abraham<BR>
Sent: 2010-4-6 (ÐÇÆÚ¶þ) 22:16<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] about ending basepairs in DNA simulation<BR>
<BR>
On 6/04/2010 11:51 PM, Wu Rongqin wrote:<BR>
> Dear all,<BR>
><BR>
> I am doing simulation on a short B-DNA which containing 11 basepairs. My<BR>
> interest is on the middle basepair in the sequence. During the<BR>
> simulation, I found severe distortion on the two basepairs at both ends,<BR>
> for example, the dihedral angle deviates from 180 degree severely.<BR>
><BR>
> Must I put any restraint to the basepairs on both ends so that I can<BR>
> simulate a basepair in a long sequence?<BR>
<BR>
That would at least depend on your force field, which you haven't told us.<BR>
<BR>
> Please give me some advice if you can.<BR>
<BR>
We can't really, since you haven't told us your force field, or how<BR>
you've prepared your termini, etc.<BR>
<BR>
Mark<BR>
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