<br clear="all">Hi all <br><br> i have done protein protein interaction and the complex structure was taken for MD simulation using Gromacs. the length of the protein was around 1100 aa. while performing mdrun step for position restrain i got error. i have carried out mdrun for 1ps and the command given for mdrun and position restrain are<br>
<br> grompp -f *.pdb -c *.gro -p top.top -o *.tpr<br><br> mdrun -v
-deffnm pr<br><br>error i got was<br><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CManju%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CManju%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CManju%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"><style>
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<p class="MsoNormal"><span style="font-size: 10pt; line-height: 115%; font-family: "Times New Roman","serif";">starting mdrun '? in water'<br>
500 steps, 1.0 ps.<br>
step 400, remaining runtime: 133
s <br>
Step 416, time 0.832 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.000577, max 0.008379 (between atoms 5530 and 5532)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
8190 8191 30.7
0.1014 0.1000 0.1000<br>
<br>
Step 419, time 0.838 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.000874, max 0.019432 (between atoms 5526 and 5527)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
112 113 31.0
0.1017 0.1002 0.1000</span></p><p class="MsoNormal"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CManju%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CManju%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CManju%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"><style>
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</p><p class="MsoNormal"><span style="font-family: "Times New Roman","serif";">Step
430, time 0.86 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 158552932798158.562500, max 14888250728513536.000000 (between atoms 1734
and 1735)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
4469 4471 66.7 0.1327
0.5535 0.1330<br>
4469 4470 69.6
0.1227 0.5336 0.1230</span></p><p class="MsoNormal"><span style="font-family: "Times New Roman","serif";">
8001 8003 47.0 0.0999
0.0998 0.1000<br>
7995 7996 30.0
0.1001 0.0999 0.1000<br>
7970 7971 34.0
0.0999 0.1002 0.1000</span></p><p class="MsoNormal">t = 0.860 ps: Water molecule starting at atom 81142 can not be settled.<br>Check
for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates</p><p class="MsoNormal"><br></p><p class="MsoNormal">could any one pls help me to overcome this problem.how give me some ideas.</p><p class="MsoNormal">looking forward for a solution. thanx in advance.<br>
<span style="font-family: "Times New Roman","serif";"></span></p>
<br><span style="font-family: "Times New Roman","serif";"></span><p></p>
<br><span style="font-size: 10pt; line-height: 115%; font-family: "Times New Roman","serif";"></span><p></p>
<br><br><br>-- <br>With Regards,<br><br>Manjulakasinathan<br>