<div>David,</div> <div> </div> <div>Thank you, you are exactly right. The .xtc file was written with precision</div> <div>10000. Does this mean that mdrun can use the same precision as shown</div> <div>in .gro file, or only use f8.3 as input?</div> <div> </div> <div>Xiaobing </div> <div> </div> <div><BR>--------------------------------<BR></div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><STRONG><EM></EM></STRONG><BR>Message: 5<BR>Date: Fri, 03 Mar 2006 19:12:43 +0100<BR>From: David van der Spoel <SPOEL@XRAY.BMC.UU.SE><BR>Subject: Re: [gmx-users] trjconv_d -f traj.xtc -dump 180.0 -o<BR>180ps.gro<BR>To: Discussion list for GROMACS users <GMX-USERS@GROMACS.ORG><BR>Message-ID: <4408871B.5090102@xray.bmc.uu.se><BR>Content-Type: text/plain; charset=UTF-8; format=flowed<BR><BR>Xiaobing Feng wrote:<BR>> Dear everyone,<BR>> <BR>> I wanted to extract a frame from traj.xtc
file<BR>> to start a new run with different .mdp file.<BR>> <BR>> I ran<BR>> trjconv_d -f traj.xtc -dump 180.0 -o 180ps.gro<BR>> <BR>> No problem, the .gro file was created, however, the<BR>> format seems wrong. It uses f9.4 for the coordinates,<BR>> instead of f8.3 as told in the manuel, so this gave<BR>> error message when I ran grompp_d.<BR>> <BR><BR>could it be that you have written the xtc file with a precision of 10000 ?<BR><BR><BR><BR>> "trjconv" generated the same output. I'm using Gromacs 3.3.<BR>> <BR>> The head part is as follows<BR>> <BR>> Generated by trjconv : SCN fluctuation t= 180.00000<BR>> 18432<BR>> 1SCN N 1 0.1511 -0.0590 0.3121<BR>> 1SCN C 2 0.1039 -0.0360 0.2088<BR>> 1SCN CH2 3 0.0430 -0.0150 0.0801<BR>> 1SCN CH2 4 0.0490 0.1360 0.0500<BR>> 1SCN C 5 0.1858 0.1779 0.0350<BR>> 1SCN N 6 0.2932 0.2211 0.0280<BR>> <BR>> <BR>> Any idea how to fix it? Many thanks in advance.<BR>> <BR>>
Yours,<BR>> <BR>> Xiaobing<BR>> </BLOCKQUOTE><p>
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