Dear Dr.Tsjerk Before doing md for generating NPT, I did an EM,the result was: poteintial energy:-2.2611160*10^(6) Max F=4.8960352*10^(4) on atom 5289 Besides I had done EM before on the same system,I just add solvent by genbox and Ions by genion. the above result is for Energy minimization after adding ions by genion.
I did what you said.but when I was generating NPT equilibration I recieved this massage: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 8.387059, max 321.381958 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5293 5294 74.4 0.1137 12.9330 0.1090 5291 5293 59.1 0.1422 32.1605 0.1390 5291 5292 103.5 0.1096 9.8747 0.1090 5289 5291 89.5 0.1383 39.2022 0.1390 5289 5290 85.7 0.1410 43.8439 0.1360 5289 5287 85.4 0.1426 44.0196 0.1390 5287 5288 90.2 0.1091 1.5178 0.1090 5285 5287 88.7 0.1391 1.9186 0.1390 5285 5286 41.8 0.1092 0.1322 0.1090 5284 5293 87.2 0.1429 21.7425 0.1390 5284 5285 92.4 0.1393 2.0880 0.1390 5277 5278 79.1 0.1532 0.5213 0.1530 5276 5284 63.0 0.1394 1.8946 0.1390 5276 5277 79.2 0.1534 0.7278 0.1530 5276 5275 79.9 0.1432 0.6036 0.1430 5274 5275 82.0 0.1431 0.3189 0.1430 5276 5272 82.1 0.1393 0.6113 0.1390 5272 5273 74.2 0.1333 0.2251 0.1330 5272 5270 77.7 0.1332 0.2428 0.1330 5270 5271 46.5 0.1091 0.1682 0.1090 5268 5270 36.9 0.1391 0.1854 0.1390 5273 5266 41.4 0.1334 0.1933 0.1330 Wrote pdb files with previous and current coordinates 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 These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Please let me know what can I do. thanks in advance On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar <[email protected]> wrote: > Hi Mohsen, > > 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 > > Cheers, > > Tsjerk > > On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" <[email protected]> > wrote: > > Dear Amit > I entered these commands for rotating box: > editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 > and then: > editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 > as a result my molecul is located out of box totally,of course drug and > protein are bind to eachother yet. > thanks in advance for your attention and reply > > On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <[email protected]> wrote: > > > Could you post the e... > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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