<br>Dear Dr.Tsjerk<br><br>Before doing md for generating NPT, I did an EM,the result was:<br>poteintial energy:-2.2611160*10^(6)<br>Max F=4.8960352*10^(4) on atom 5289<br>Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion.<br>
the above result is for Energy minimization after adding ions by genion.<br><br>I did what you said.but when I was generating NPT equilibration <br>I recieved this massage:<br><br><br>Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 8.387059, max 321.381958 (between atoms 5289 and 5290)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 5293 5294 74.4 0.1137 12.9330 0.1090<br>
5291 5293 59.1 0.1422 32.1605 0.1390<br> 5291 5292 103.5 0.1096 9.8747 0.1090<br> 5289 5291 89.5 0.1383 39.2022 0.1390<br> 5289 5290 85.7 0.1410 43.8439 0.1360<br>
5289 5287 85.4 0.1426 44.0196 0.1390<br> 5287 5288 90.2 0.1091 1.5178 0.1090<br> 5285 5287 88.7 0.1391 1.9186 0.1390<br> 5285 5286 41.8 0.1092 0.1322 0.1090<br>
5284 5293 87.2 0.1429 21.7425 0.1390<br> 5284 5285 92.4 0.1393 2.0880 0.1390<br> 5277 5278 79.1 0.1532 0.5213 0.1530<br> 5276 5284 63.0 0.1394 1.8946 0.1390<br>
5276 5277 79.2 0.1534 0.7278 0.1530<br> 5276 5275 79.9 0.1432 0.6036 0.1430<br> 5274 5275 82.0 0.1431 0.3189 0.1430<br> 5276 5272 82.1 0.1393 0.6113 0.1390<br>
5272 5273 74.2 0.1333 0.2251 0.1330<br> 5272 5270 77.7 0.1332 0.2428 0.1330<br> 5270 5271 46.5 0.1091 0.1682 0.1090<br> 5268 5270 36.9 0.1391 0.1854 0.1390<br>
5273 5266 41.4 0.1334 0.1933 0.1330<br>Wrote pdb files with previous and current coordinates<br>step 0Warning: 1-4 interaction between 5272 and 5293 at distance 22.443 which is larger than the 1-4 table size 2.400 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>Please let me know what can I do.<br>
thanks in advance <br><br><br><br><br><br><br><br><br><br><br><br><br><br><div class="gmail_quote">On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><p>Hi Mohsen,</p>
<p>I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p></p><blockquote type="cite"><div class="im">On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>> wrote:<br><br>Dear Amit<br>
I entered these commands for rotating box:<br>
editconf -f conf.gro -o output.pdb -rotate 0 0 25.4<br>and then:<br>editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 <br>as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet.<br>
thanks in advance for your attention and reply</div><p><font color="#500050">
On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>> wrote:
>
> Could you post the e...</font></p><div class="im"><br>--<br>
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