<DIV>Date: Thu, 07 Jun 2012 07:59:27 -0400<BR>From: "Justin A. Lemkul" <<A href="mailto:jalemkul@vt.edu" target=_blank><FONT color=#1e5494>jalemkul@vt.<WBR>edu</FONT></A>><BR>Subject: Re: [gmx-users] How to set up constraint distcance pulling<BR>To: Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org" target=_blank><FONT color=#1e5494>gmx-users@gr<WBR>omacs.org</FONT></A>><BR>Message-ID: <<A href="mailto:4FD0979F.4020702@vt.edu" target=_blank><FONT color=#1e5494>4FD0979F.402<WBR>0702@vt.edu</FONT></A>><BR>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<BR>Thank you very much!</DIV>
<DIV><BR>On 6/7/12 7:38 AM, xiaowu759 wrote:<BR>>> Dear gmxers,<BR>>> I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of<BR>>> distance between the COMs of two molecules. However, quite strange resuluts are<BR>>> generated, i.e., the distance can not be fixed at the value defined by<BR>>>pull_init1. The pull opinions are given below. Could you please tell me how to<BR>>> deal with this? Thanks a lot for any reply.<BR><BR>>How far away from the target value are the results in terms of COM distance?<BR>A: very far, several hundreds vs. 0.8 nm<BR>>> Chaofu Wu<BR>>> ;Pull opinions<BR>>> pull = constraint<BR>>> pull_geometry = distance<BR>>> ;pull_dim = Y Y Y<BR><BR>>The comment here has no effect; pull_dim defaults to "Y Y Y."<BR>A: Yes<BR>>> pull_group0 = r1<BR>> >pull_group1 = r2<BR>> >pull_nstxout = 0<BR>> >pull_nstfout = 5<BR>>> pull_init1 = 0.80<BR><BR>>How does this pull_init1 value compare to the COM separation in the coordinate <BR>>file? If the distance is not very close, the constraint algorithm may fail.<BR>A: The COM separation in the coordinate file is 0.567 nm, which should be not too larger than 0.80 defined by pull_init1. <BR>>-Justin<BR><BR>-- <BR>========================================<BR><BR>Justin A. Lemkul, Ph.D.<BR>Research Scientist<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank><FONT color=#1e5494>http://www.b<WBR>evanlab.bioc<WBR>hem.vt.edu/P<WBR>ages/Persona<WBR>l/justin</FONT></A></DIV>
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