Re: [gmx-users] Signal: Segmentation faul
shikha agarwal wrote: hi, HAPPY NEW YEAR I am experiencing a segmentation fault during mdrun in equlibration step . error Wrote pdb files with previous and current coordinates [shikha-desktop:01719] *** Process received signal *** [shikha-desktop:01719] Signal: Segmentation fault (11) [shikha-desktop:01719] Signal code: Address not mapped (1) [shikha-desktop:01719] Failing at address: 0x8d22a70 [shikha-desktop:01719] [ 0] [0xb87410] [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789] [shikha-desktop:01719] *** End of error message *** Segmentation fault bottom lines of my .log file after energy minimization is this Step Time Lambda 1135711357.00.0 Step Time Lambda 1135811358.00.0 Step Time Lambda 1135911359.00.0 Step Time Lambda 1136011360.00.0 Step Time Lambda 1136111361.00.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 11362 steps, but did not reach the requested Fmax < 1000. Potential Energy = -5.4871900e+06 Maximum force = 3.9830833e+03 on atom 4511 Norm of force = 1.9521437e+01 Well, EM completed, but the forces are still very high, indicating that the system is likely not yet stable. Look at the structure to see what might be causing problems around atom 4511. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NPT
Dear All In doing umbrella sampling ,when I want to generate NPT every thing is going well but one error is occuring in the first. please let me know how can I solve this problem. Is it usefull to extend the degree which is defined in .mdp file? Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 40.60.1143 0.1260 0.1140 5293 5294 82.70.1221 2613.7048 0.1090 5291 5293 77.20.1517 6084.3052 0.1390 5291 5292 101.00.1117 1519.0425 0.1090 5289 5291 87.70.1353 6893.7969 0.1390 5289 5290 88.40.1437 7531.5815 0.1360 5289 5287 88.40.1456 7542.5801 0.1390 5287 5288 89.70.1092 381.6111 0.1090 5285 5287 92.30.1395 355.0215 0.1390 5285 5286 123.80.1101 44.8588 0.1090 5284 5293 89.00.1478 4606.4570 0.1390 5284 5285 79.30.1402 173.6082 0.1390 5278 5279 78.90.1529 1.1246 0.1530 5277 5278 122.90.1545 13.1470 0.1530 5276 5284 84.90.1422 159.0514 0.1390 5276 5277 68.40.1543 90.8518 0.1530 5276 5275 39.50.1439 72.5391 0.1430 5274 5275 103.70.1436 21.6098 0.1430 5273 5274 108.60.1394 3.3410 0.1390 5276 5272 45.70.1402 80.7004 0.1390 5272 5273 127.30.1340 14.2414 0.1330 5272 5270 69.80.1336 12.6282 0.1330 5270 5271 113.30.1092 0.2532 0.1090 5268 5270 104.50.1391 0.2727 0.1390 5268 5269 44.00.1091 0.1624 0.1090 5273 5266 58.50.1342 14.0148 0.1330 5265 5268 36.70.1394 0.1774 0.1390 Actually md is crush,of course I think so. Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT
mohsen ramezanpour wrote: Dear All In doing umbrella sampling ,when I want to generate NPT every thing is going well but one error is occuring in the first. please let me know how can I solve this problem. Is it usefull to extend the degree which is defined in .mdp file? No. The constraints are failing, but they are not the problem that needs to be fixed. Please see: http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 40.60.1143 0.1260 0.1140 5293 5294 82.70.1221 2613.7048 0.1090 5291 5293 77.20.1517 6084.3052 0.1390 5291 5292 101.00.1117 1519.0425 0.1090 5289 5291 87.70.1353 6893.7969 0.1390 5289 5290 88.40.1437 7531.5815 0.1360 5289 5287 88.40.1456 7542.5801 0.1390 5287 5288 89.70.1092 381.6111 0.1090 5285 5287 92.30.1395 355.0215 0.1390 5285 5286 123.80.1101 44.8588 0.1090 5284 5293 89.00.1478 4606.4570 0.1390 5284 5285 79.30.1402 173.6082 0.1390 5278 5279 78.90.1529 1.1246 0.1530 5277 5278 122.90.1545 13.1470 0.1530 5276 5284 84.90.1422 159.0514 0.1390 5276 5277 68.40.1543 90.8518 0.1530 5276 5275 39.50.1439 72.5391 0.1430 5274 5275 103.70.1436 21.6098 0.1430 5273 5274 108.60.1394 3.3410 0.1390 5276 5272 45.70.1402 80.7004 0.1390 5272 5273 127.30.1340 14.2414 0.1330 5272 5270 69.80.1336 12.6282 0.1330 5270 5271 113.30.1092 0.2532 0.1090 5268 5270 104.50.1391 0.2727 0.1390 5268 5269 44.00.1091 0.1624 0.1090 5273 5266 58.50.1342 14.0148 0.1330 5265 5268 36.70.1394 0.1774 0.1390 Actually md is crush,of course I think so. Thanks in advance -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The sum of the O-H distancesof the backbone hydrogen bonds ROH
On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote: Dear all, I have a protein in water and i have simulated it for few nanoseconds and i now i wanted to monitor the The sum of the O-H distances (in Å) of the backbone hydrogen bonds ROH:i dono how to extract the value from the trajectory file.Any siuggestion please.Thanks in advance Look in section 7.4 of the manual for a suitable tool for extracting the raw distances. You'll need some other non-GROMACS tool to add them up. Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT
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Re: [gmx-users] NPT
On 1/3/11, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: >> Dear All >> In doing umbrella sampling ,when I want to generate NPT every thing is >> going well but one error is occuring in the first. >> please let me know how can I solve this problem. >> Is it usefull to extend the degree which is defined in .mdp file? > > No. The constraints are failing, but they are not the problem that needs to > be > fixed. Please see: > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up >Dear Justin I looked at that page,I changed timestep to 0.001 and even to 0.0005 but it did not have any positive effect,I think the .mdp file in umbrella sampling page is not proper in my problem(protein-ligand docking),what do you think? thanks in advance > -Justin > >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.002537, max 0.119994 (between atoms 5293 and 5294) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> starting mdrun 'Protein in water' >> 5 steps,100.0 ps. >> >> Step 0, time 0 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >>5264 5263 40.60.1143 0.1260 0.1140 >>5293 5294 82.70.1221 2613.7048 0.1090 >>5291 5293 77.20.1517 6084.3052 0.1390 >>5291 5292 101.00.1117 1519.0425 0.1090 >>5289 5291 87.70.1353 6893.7969 0.1390 >>5289 5290 88.40.1437 7531.5815 0.1360 >>5289 5287 88.40.1456 7542.5801 0.1390 >>5287 5288 89.70.1092 381.6111 0.1090 >>5285 5287 92.30.1395 355.0215 0.1390 >>5285 5286 123.80.1101 44.8588 0.1090 >>5284 5293 89.00.1478 4606.4570 0.1390 >>5284 5285 79.30.1402 173.6082 0.1390 >>5278 5279 78.90.1529 1.1246 0.1530 >>5277 5278 122.90.1545 13.1470 0.1530 >>5276 5284 84.90.1422 159.0514 0.1390 >>5276 5277 68.40.1543 90.8518 0.1530 >>5276 5275 39.50.1439 72.5391 0.1430 >>5274 5275 103.70.1436 21.6098 0.1430 >>5273 5274 108.60.1394 3.3410 0.1390 >>5276 5272 45.70.1402 80.7004 0.1390 >>5272 5273 127.30.1340 14.2414 0.1330 >>5272 5270 69.80.1336 12.6282 0.1330 >>5270 5271 113.30.1092 0.2532 0.1090 >>5268 5270 104.50.1391 0.2727 0.1390 >>5268 5269 44.00.1091 0.1624 0.1090 >>5273 5266 58.50.1342 14.0148 0.1330 >>5265 5268 36.70.1394 0.1774 0.1390 >> >> Actually md is crush,of course I think so. >> Thanks in advance > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT
mohsen ramezanpour wrote: On 1/3/11, Justin A. Lemkul wrote: mohsen ramezanpour wrote: Dear All In doing umbrella sampling ,when I want to generate NPT every thing is going well but one error is occuring in the first. please let me know how can I solve this problem. Is it usefull to extend the degree which is defined in .mdp file? No. The constraints are failing, but they are not the problem that needs to be fixed. Please see: http://www.gromacs.org/Documentation/Terminology/Blowing_Up Dear Justin I looked at that page,I changed timestep to 0.001 and even to 0.0005 but it did not have any positive effect,I think the .mdp file in umbrella sampling page is not proper in my problem(protein-ligand docking),what do you think? If you're taking it directly from the tutorial, it may need some tweaking to suit your needs. But if your system is failing immediately (step 0), it is far more likely that there is a physical instability that cannot be avoided by simply changing the time step. Please see the "Diagnosing an Unstable System" section on that page. It contains basically all the advice that one normally gets in this situation. -Justin thanks in advance -Justin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.002537, max 0.119994 (between atoms 5293 and 5294) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'Protein in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5264 5263 40.60.1143 0.1260 0.1140 5293 5294 82.70.1221 2613.7048 0.1090 5291 5293 77.20.1517 6084.3052 0.1390 5291 5292 101.00.1117 1519.0425 0.1090 5289 5291 87.70.1353 6893.7969 0.1390 5289 5290 88.40.1437 7531.5815 0.1360 5289 5287 88.40.1456 7542.5801 0.1390 5287 5288 89.70.1092 381.6111 0.1090 5285 5287 92.30.1395 355.0215 0.1390 5285 5286 123.80.1101 44.8588 0.1090 5284 5293 89.00.1478 4606.4570 0.1390 5284 5285 79.30.1402 173.6082 0.1390 5278 5279 78.90.1529 1.1246 0.1530 5277 5278 122.90.1545 13.1470 0.1530 5276 5284 84.90.1422 159.0514 0.1390 5276 5277 68.40.1543 90.8518 0.1530 5276 5275 39.50.1439 72.5391 0.1430 5274 5275 103.70.1436 21.6098 0.1430 5273 5274 108.60.1394 3.3410 0.1390 5276 5272 45.70.1402 80.7004 0.1390 5272 5273 127.30.1340 14.2414 0.1330 5272 5270 69.80.1336 12.6282 0.1330 5270 5271 113.30.1092 0.2532 0.1090 5268 5270 104.50.1391 0.2727 0.1390 5268 5269 44.00.1091 0.1624 0.1090 5273 5266 58.50.1342 14.0148 0.1330 5265 5268 36.70.1394 0.1774 0.1390 Actually md is crush,of course I think so. Thanks in advance -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
Dear Justin and Chris very thanks for your reply and guidance. I did all the steps successfully. then I used (./my_tool -f final.xtc -o final.pdb -b 300 -e 350), the final.pdb file was created without problem. when I opened final.pdb file by text editor, order of waters and ions in final.pdb was like final.xtc (waters are before ions). my purpose was to reorder water molecules with Na+ ions in final.xtc file as at first 1-1867 complex (protein and dna) 1868 - 24085 SOL (water molecules) 24086 - 24099Na+ (ions) after reordering 1-1867 complex (protein and dna) 1868 -1881 Na+ (ions) 1882 - 24099 SOL (water molecules) but this wasn't done. Is there problem in modification made in gmx_trjconv.c or same my_tool.c file: ### Now go to line 1264 of the file and replace this: for(i=0; i-- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
for example ordering in final.pdb is as follows: ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00 0.00 ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00 0.00 ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00 0.00 ATOM 1859 N3 DG3 X 86 14.160 46.250 20.930 1.00 0.00 ATOM 1860 C4 DG3 X 86 13.780 45.460 19.890 1.00 0.00 ATOM 1861 C3' DG3 X 86 10.130 43.520 22.330 1.00 0.00 ATOM 1862 H3' DG3 X 86 9.350 42.780 22.490 1.00 0.00 ATOM 1863 C2' DG3 X 86 10.400 43.920 20.880 1.00 0.00 ATOM 1864 H2'1 DG3 X 86 10.450 43.060 20.220 1.00 0.00 ATOM 1865 H2'2 DG3 X 86 9.720 44.720 20.580 1.00 0.00 ATOM 1866 O3' DG3 X 86 9.680 44.620 23.090 1.00 0.00 ATOM 1867 H3T DG3 X 86 8.790 44.770 22.760 1.00 0.00 ATOM 1868 OW SOL X 87 6.340 24.560 33.150 1.00 0.00 ATOM 1869 HW1 SOL X 87 6.550 24.130 33.980 1.00 0.00 ATOM 1870 HW2 SOL X 87 6.590 25.470 33.290 1.00 0.00 ATOM 1871 OW SOL X 88 9.070 15.110 50.520 1.00 0.00 ATOM 1872 HW1 SOL X 88 8.250 15.450 50.870 1.00 0.00 ATOM 1873 HW2 SOL X 88 9.210 15.590 49.700 1.00 0.00 ATOM 1874 OW SOL X 89 56.650 30.810 11.740 1.00 0.00 ATOM 1875 HW1 SOL X 89 56.550 30.850 12.690 1.00 0.00 ATOM 1876 HW2 SOL X 89 55.930 31.350 11.390 1.00 0.00 while I want that ordering be as follows: ATOM 1856 N2 DG386 18.350 45.720 25.030 1.00 0.00 ATOM 1857 H21 DG386 19.090 46.250 24.600 1.00 0.00 ATOM 1858 H22 DG386 18.200 45.590 26.020 1.00 0.00 ATOM 1859 N3 DG386 16.690 44.090 24.990 1.00 0.00 ATOM 1860 C4 DG386 15.990 43.270 24.170 1.00 0.00 ATOM 1861 C3' DG386 12.600 41.300 27.150 1.00 0.00 ATOM 1862 H3' DG386 11.700 40.720 26.920 1.00 0.00 ATOM 1863 C2' DG386 12.940 42.170 25.940 1.00 0.00 ATOM 1864 1H2' DG386 12.480 41.850 25.010 1.00 0.00 ATOM 1865 2H2' DG386 12.630 43.200 26.160 1.00 0.00 ATOM 1866 O3' DG386 12.400 42.100 28.290 1.00 0.00 ATOM 1867 H3T DG386 12.270 41.510 29.030 1.00 0.00 ATOM 1868 Na Na87 9.520 12.960 25.870 1.00 0.00 ATOM 1869 Na Na88 10.890 27.910 9.650 1.00 0.00 ATOM 1870 Na Na89 22.150 55.600 31.600 1.00 0.00 ATOM 1871 Na Na90 36.340 1.500 6.140 1.00 0.00 ATOM 1872 Na Na91 38.910 14.970 5.700 1.00 0.00 ATOM 1873 Na Na92 37.660 9.000 16.270 1.00 0.00 ATOM 1874 Na Na93 25.770 23.110 23.230 1.00 0.00 ATOM 1875 Na Na94 53.000 2.470 52.760 1.00 0.00 ATOM 1876 Na Na95 43.750 28.050 1.000 1.00 0.00 ATOM 1877 Na Na96 44.200 48.440 0.470 1.00 0.00 ATOM 1878 Na Na97 37.770 56.870 33.540 1.00 0.00 ATOM 1879 Na Na98 54.240 26.650 18.640 1.00 0.00 ATOM 1880 Na Na99 61.510 35.570 8.100 1.00 0.00 ATOM 1881 Na Na 100 61.950 46.140 43.640 1.00 0.00 ATOM 1882 OW SOL 101 28.260 19.060 16.930 1.00 0.00 ATOM 1883 HW1 SOL 101 28.610 19.950 16.980 1.00 0.00 ATOM 1884 HW SOL 101 27.370 19.140 17.290 1.00 0.00 ATOM 1885 OW SOL 102 34.220 11.510 13.510 1.00 0.00 ATOM 1886 HW1 SOL 102 34.420 11.880 12.660 1.00 0.00 ATOM 1887 HW2 SOL 102 34.660 12.090 14.140 1.00 0.00 ATOM 1888 OW SOL 103 18.620 9.650 16.990 1.00 0.00 ATOM 1889 HW1 SOL 103 18.280 8.870 17.430 1.00 0.00 ATOM 1890 HW2 SOL 103 19.560 9.620 17.160 1.00 0.00 ATOM 1891 OW SOL 104 22.090 26.530 6.110 1.00 0.00 ATOM 1892 HW1 SOL 104 21.560 25.810 6.460 1.00 0.00 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_sas values for peptide in water and in DPC micelle
Dear all, Firstly, I wish you a happy new year filled with joy, health and lots of finding !! Now my question: I have simulated one peptide (25 AA length + N- and C- caps) in two environment: one in bulk water TIP3P water (A) and one with a DPC micelle in water (B). My peptide keep in the two simulations a very similar secondary structure (alpha helix). The peptide in the system B, during the last 50 ns of the simulation time, is located in the micelle/water interface in the little crevice formed by the DPC hydrophobic chain and remains in the same place. I would like to compute the accessible surface area with respect to solvent for some residues of the peptide and especially for the single TRP of the peptide (TRP553) and compare with the SA obtained for the same peptide in water. By examining several configurations of the peptide in the B system at the end of the simulation (~150 ns) with pymol, I found that TRP553 residue is mainly in contact with the DPC micelle hydrophobic core and is not fully exposed to the solvent. So i expect that the average SA value for TRP553 (and for the others residues) in system B will be smaller than the values obtained for the same residues in the system A. I used the following command for the two systems g_sas_mpi -f *.xtc -s md_0_24.tpr -b 99500 -e 10 -dt 10 -or mTM10-TIP3_per_residu_TRP553_SAS.xvg -oa mTM10-TIP3_per_atom_TRP553_SAS.xvg -n System_TRP553.ndx I choose the option 2 (Protein-H) in the menu. It is the correct combination for g_sas ? The output of g_sas (gmx 4.5.3) are shown below for the two systems. Average values are computed for A and B from the last 500 ps (extracted every 10 frames -> 50 values) System A @ s0 legend "Average (nm\S2\N)" @ s1 legend "Standard deviation (nm\S2\N)" 5450.723556 0.0709648 5460.851864 0.0780804 5470.782327 0.0548426 548 0.97012 0.0836672 5490.339449 0.0611941 5500.839293 0.0795415 551 1.34999 0.104301 5520.708079 0.0693484 553 1.95306 0.135732 554 1.02126 0.0899936 555 0.32233 0.0755605 5560.643128 0.0645317 5570.842983 0.0683777 558 1.37868 0.107237 5590.972423 0.108448 5600.875918 0.0707144 561 0.56353 0.0494754 5620.979795 0.0875196 563 0.6764 0.0599796 5640.792996 0.0830322 565 1.29532 0.123898 5660.493239 0.0679436 5670.991596 0.0743836 568 1.71456 0.121319 5690.943561 0.0747361 570 1.12007 0.0511916 5710.572433 0.0343254 System B @ s0 legend "Average (nm\S2\N)" @ s1 legend "Standard deviation (nm\S2\N)" 5450.721979 0.0582663 5460.905305 0.0508979 5470.785995 0.053198 5480.944034 0.0688671 5490.394531 0.0606229 5500.803279 0.0667054 551 1.38402 0.083296 5520.9202830.06624 553 1.824 0.127784 5540.688272 0.0821362 555 0.50046 0.0694137 5560.870991 0.0733946 5570.765114 0.0651865 558 1.27511 0.116357 559 1.14207 0.0791716 5600.950344 0.0677436 5610.564978 0.052539 5620.983167 0.0857281 5630.670499 0.0607886 5640.814746 0.0638795 565 1.16659 0.0778935 5660.551229 0.0534253 567 1.02231 0.0561598 568 1.69817 0.115372 5690.878103 0.0621447 5700.982666 0.0652861 5710.742895 0.0373423 As you can see, it is not the case since the SA values are not significantly different between the two systems, i don t understand why. Did i use use the good combination for g_sas ? Thank you in advance for your help/advices. Stephane -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas values for peptide in water and in DPC micelle
sa wrote: Dear all, Firstly, I wish you a happy new year filled with joy, health and lots of finding !! Now my question: I have simulated one peptide (25 AA length + N- and C- caps) in two environment: one in bulk water TIP3P water (A) and one with a DPC micelle in water (B). My peptide keep in the two simulations a very similar secondary structure (alpha helix). The peptide in the system B, during the last 50 ns of the simulation time, is located in the micelle/water interface in the little crevice formed by the DPC hydrophobic chain and remains in the same place. I would like to compute the accessible surface area with respect to solvent for some residues of the peptide and especially for the single TRP of the peptide (TRP553) and compare with the SA obtained for the same peptide in water. By examining several configurations of the peptide in the B system at the end of the simulation (~150 ns) with pymol, I found that TRP553 residue is mainly in contact with the DPC micelle hydrophobic core and is not fully exposed to the solvent. So i expect that the average SA value for TRP553 (and for the others residues) in system B will be smaller than the values obtained for the same residues in the system A. I used the following command for the two systems g_sas_mpi -f *.xtc -s md_0_24.tpr -b 99500 -e 10 -dt 10 -or mTM10-TIP3_per_residu_TRP553_SAS.xvg -oa mTM10-TIP3_per_atom_TRP553_SAS.xvg -n System_TRP553.ndx I choose the option 2 (Protein-H) in the menu. It is the correct combination for g_sas ? The output of g_sas (gmx 4.5.3) are shown below for the two systems. Average values are computed for A and B from the last 500 ps (extracted every 10 frames -> 50 values) System A @ s0 legend "Average (nm\S2\N)" @ s1 legend "Standard deviation (nm\S2\N)" 5450.723556 0.0709648 5460.851864 0.0780804 5470.782327 0.0548426 548 0.97012 0.0836672 5490.339449 0.0611941 5500.839293 0.0795415 551 1.34999 0.104301 5520.708079 0.0693484 553 1.95306 0.135732 554 1.02126 0.0899936 555 0.32233 0.0755605 5560.643128 0.0645317 5570.842983 0.0683777 558 1.37868 0.107237 5590.972423 0.108448 5600.875918 0.0707144 561 0.56353 0.0494754 5620.979795 0.0875196 563 0.6764 0.0599796 5640.792996 0.0830322 565 1.29532 0.123898 5660.493239 0.0679436 5670.991596 0.0743836 568 1.71456 0.121319 5690.943561 0.0747361 570 1.12007 0.0511916 5710.572433 0.0343254 System B @ s0 legend "Average (nm\S2\N)" @ s1 legend "Standard deviation (nm\S2\N)" 5450.721979 0.0582663 5460.905305 0.0508979 5470.785995 0.053198 5480.944034 0.0688671 5490.394531 0.0606229 5500.803279 0.0667054 551 1.38402 0.083296 5520.9202830.06624 553 1.824 0.127784 5540.688272 0.0821362 555 0.50046 0.0694137 5560.870991 0.0733946 5570.765114 0.0651865 558 1.27511 0.116357 559 1.14207 0.0791716 5600.950344 0.0677436 5610.564978 0.052539 5620.983167 0.0857281 5630.670499 0.0607886 5640.814746 0.0638795 565 1.16659 0.0778935 5660.551229 0.0534253 567 1.02231 0.0561598 568 1.69817 0.115372 5690.878103 0.0621447 5700.982666 0.0652861 5710.742895 0.0373423 As you can see, it is not the case since the SA values are not significantly different between the two systems, i don t understand why. Did i use use the good combination for g_sas ? No. If you have a DPC micelle, it needs to be part of the calculation group, as well. The output group can then be whatever you want it to be. But if you don't consider the micelle, g_sas will happily calculate SASA as if your peptide were simply in water. Your results seem to agree. g_sas -h: ..."The calculation group should always consists of all the non-solvent atoms in the system"... -Justin Thank you in advance for your help/advices. Stephane -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
Hey Leila,
Why all the fuzz? You can do this with trjconv using an index file.
The following oneliner (:$) should write you the index file you need.
python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'
Hope it helps,
Tsjerk
On Mon, Jan 3, 2011 at 3:17 PM, leila karami wrote:
> for example ordering in final.pdb is as follows:
>
> ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00
> 0.00
> ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00
> 0.00
> ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00
> 0.00
> ATOM 1859 N3 DG3 X 86 14.160 46.250 20.930 1.00
> 0.00
> ATOM 1860 C4 DG3 X 86 13.780 45.460 19.890 1.00
> 0.00
> ATOM 1861 C3' DG3 X 86 10.130 43.520 22.330 1.00
> 0.00
> ATOM 1862 H3' DG3 X 86 9.350 42.780 22.490 1.00
> 0.00
> ATOM 1863 C2' DG3 X 86 10.400 43.920 20.880 1.00
> 0.00
> ATOM 1864 H2'1 DG3 X 86 10.450 43.060 20.220 1.00
> 0.00
> ATOM 1865 H2'2 DG3 X 86 9.720 44.720 20.580 1.00
> 0.00
> ATOM 1866 O3' DG3 X 86 9.680 44.620 23.090 1.00
> 0.00
> ATOM 1867 H3T DG3 X 86 8.790 44.770 22.760 1.00
> 0.00
> ATOM 1868 OW SOL X 87 6.340 24.560 33.150 1.00
> 0.00
> ATOM 1869 HW1 SOL X 87 6.550 24.130 33.980 1.00
> 0.00
> ATOM 1870 HW2 SOL X 87 6.590 25.470 33.290 1.00
> 0.00
> ATOM 1871 OW SOL X 88 9.070 15.110 50.520 1.00
> 0.00
> ATOM 1872 HW1 SOL X 88 8.250 15.450 50.870 1.00
> 0.00
> ATOM 1873 HW2 SOL X 88 9.210 15.590 49.700 1.00
> 0.00
> ATOM 1874 OW SOL X 89 56.650 30.810 11.740 1.00
> 0.00
> ATOM 1875 HW1 SOL X 89 56.550 30.850 12.690 1.00
> 0.00
> ATOM 1876 HW2 SOL X 89 55.930 31.350 11.390 1.00 0.00
>
> while I want that ordering be as follows:
>
> ATOM 1856 N2 DG3 86 18.350 45.720 25.030 1.00 0.00
> ATOM 1857 H21 DG3 86 19.090 46.250 24.600 1.00 0.00
> ATOM 1858 H22 DG3 86 18.200 45.590 26.020 1.00 0.00
> ATOM 1859 N3 DG3 86 16.690 44.090 24.990 1.00 0.00
> ATOM 1860 C4 DG3 86 15.990 43.270 24.170 1.00 0.00
> ATOM 1861 C3' DG3 86 12.600 41.300 27.150 1.00 0.00
> ATOM 1862 H3' DG3 86 11.700 40.720 26.920 1.00 0.00
> ATOM 1863 C2' DG3 86 12.940 42.170 25.940 1.00 0.00
> ATOM 1864 1H2' DG3 86 12.480 41.850 25.010 1.00 0.00
> ATOM 1865 2H2' DG3 86 12.630 43.200 26.160 1.00 0.00
> ATOM 1866 O3' DG3 86 12.400 42.100 28.290 1.00 0.00
> ATOM 1867 H3T DG3 86 12.270 41.510 29.030 1.00 0.00
> ATOM 1868 Na Na 87 9.520 12.960 25.870 1.00 0.00
> ATOM 1869 Na Na 88 10.890 27.910 9.650 1.00 0.00
> ATOM 1870 Na Na 89 22.150 55.600 31.600 1.00 0.00
> ATOM 1871 Na Na 90 36.340 1.500 6.140 1.00 0.00
> ATOM 1872 Na Na 91 38.910 14.970 5.700 1.00 0.00
> ATOM 1873 Na Na 92 37.660 9.000 16.270 1.00 0.00
> ATOM 1874 Na Na 93 25.770 23.110 23.230 1.00 0.00
> ATOM 1875 Na Na 94 53.000 2.470 52.760 1.00 0.00
> ATOM 1876 Na Na 95 43.750 28.050 1.000 1.00 0.00
> ATOM 1877 Na Na 96 44.200 48.440 0.470 1.00 0.00
> ATOM 1878 Na Na 97 37.770 56.870 33.540 1.00 0.00
> ATOM 1879 Na Na 98 54.240 26.650 18.640 1.00 0.00
> ATOM 1880 Na Na 99 61.510 35.570 8.100 1.00 0.00
> ATOM 1881 Na Na 100 61.950 46.140 43.640 1.00 0.00
> ATOM 1882 OW SOL 101 28.260 19.060 16.930 1.00 0.00
> ATOM 1883 HW1 SOL 101 28.610 19.950 16.980 1.00 0.00
> ATOM 1884 HW SOL 101 27.370 19.140 17.290 1.00 0.00
> ATOM 1885 OW SOL 102 34.220 11.510 13.510 1.00 0.00
> ATOM 1886 HW1 SOL 102 34.420 11.880 12.660 1.00 0.00
> ATOM 1887 HW2 SOL 102 34.660 12.090 14.140 1.00 0.00
> ATOM 1888 OW SOL 103 18.620 9.650 16.990 1.00 0.00
> ATOM 1889 HW1 SOL 103 18.280 8.870 17.430 1.00 0.00
> ATOM 1890 HW2 SOL 103 19.560 9.620 17.160 1.00 0.00
> ATOM 1891 OW SOL 104 22.090 26.530 6.110 1.00 0.00
> ATOM 1892 HW1 SOL 104 21.560 25.810 6.460 1.00 0.00
>
> --
> gmx-users mailing list gmx-us...@gromacs.org
> 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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomo
[gmx-users] Average box size
Hi all I did NPT simulation for 30 ns using triclinic box (-angles 88.30, 107.40, 112.20) and Isotropic pressure coupling. Now i want to use average box size for production run (NVT). But I am confused because i am not able to get the meaning of the output values of the log file. Log file output. <== ### ==> < A V E R A G E S > <== ### ==> Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.31715e+022.35558e+031.63083e+025.15266e+031.79003e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.63211e+042.86765e+04 -1.72320e+05 -4.98704e+04 -1.66800e+05 Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd () 1.27874e+04 -1.54012e+051.49958e+021.07033e+000.0e+00 Box-X Box-Y Box-Z Volume Density (SI) 4.44479e+004.49781e+004.88259e+009.76118e+011.04364e+03 If Box-X Box-Y Box-Z represent average value of a b c then volume does not correspond to my triclinic box because its just multiplication of Box-X Box-Y Box-Z. So Please can anybody help me which volume should I consider for next NVT production run. Any help in this regard would be highly appreciated. Thanks & Regards, Navjeet Ahalawat -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Average box size
Hi Navjeet, The box is defined as a triangular matrix, so the volume equals the product of the diagonal elements. Hope it helps, Tsjerk On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat" wrote: Hi all I did NPT simulation for 30 ns using triclinic box (-angles 88.30, 107.40, 112.20) and Isotropic pressure coupling. Now i want to use average box size for production run (NVT). But I am confused because i am not able to get the meaning of the output values of the log file. Log file output. <== ### ==> < A V E R A G E S > <== ### ==> Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell. LJ-14 9.31715e+022.35558e+031.63083e+025.15266e+031.79003e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 1.63211e+042.86765e+04 -1.72320e+05 -4.98704e+04 -1.66800e+05 Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd () 1.27874e+04 -1.54012e+051.49958e+021.07033e+000.0e+00 Box-X Box-Y Box-Z Volume Density (SI) 4.44479e+004.49781e+004.88259e+009.76118e+011.04364e+03 If Box-X Box-Y Box-Z represent average value of a b c then volume does not correspond to my triclinic box because its just multiplication of Box-X Box-Y Box-Z. So Please can anybody help me which volume should I consider for next NVT production run. Any help in this regard would be highly appreciated. Thanks & Regards, Navjeet Ahalawat -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
Dear Tsjerk
thanks for your reply
I have not experience in using python.
in [python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'].
r.ndx contains all the atoms. is it true?
why did you use r,a,b,c=range,1868,24086,24100.
is r,a,b,c=range,1867,24085,24099 wrong?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
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[gmx-users] eordering of water molecules with Na+ ions coordinates in xtc file
It seems like Tsjerk has a better solution. It appears that you need only to have an index group in which the atoms are ordered in the output order that you desire. Therefore, if you wanted to reverse the order of the first 3 atoms, you would create an index file like this: [ my_group ] 3 2 1 Just create something like that for your group. Looks like Tsjerk has even showed you how to create the index file that you want. You would use this with the regular version of trjconv. I didn't know that this was possible. Chris. -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file
Hi Leila,
r.ndx would be the index file indeed. Sorry for not explicitly mentioning
that. For the rest, the most important question is 'did it work?' Knowing
python is not so important, unless you're determined to understand how it
works :) As for the numbers, python always goes up to, not including. So, to
get a series from 1 to 10, you'd do range(1,11). The line builds three
ranges, so I aliased the function 'range' to 'r' to shorten the line.
There's a lot of malpractice in that line ;) but it works, right?
By the way, Python is worth your while. It's actually renowned for it's
clarity. But anything can be obscured :p
Cheers,
Tsjerk
On Jan 3, 2011 6:39 PM, "leila karami" wrote:
Dear Tsjerk
thanks for your reply
I have not experience in using python.
in [python -c
'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'].
r.ndx contains all the atoms. is it true?
why did you use r,a,b,c=range,1868,24086,24100.
is r,a,b,c=range,1867,24085,24099 wrong?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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[gmx-users] Trifluoroethanol-Ethanol mixtures study
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Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
On 4/01/2011 9:39 AM, Marcelo Silva wrote: Hi everybody, I am starting to simulate ethanol-trifluoroethanol mixtures with opls aa, but TFE is not defined in the opls rtp file, so I added a new entry. I would like to confirm if the way the charge groups are defined for ethanol are mantained for TFE: CB 1 HB11 HB21 HB31 CA 2 HA1 2 HA2 2 OH 2 HO 2 Because in the case of TFE the charge groups don't add to zero. Hence the charges are not assigned correctly. More is required than substituting OH for H in an ethane molecule, for a carbon with an electron-withdrawing group like -OH will have a more negative partial charge than the other carbon. TFE and ethanol will follow the same pattern of charge distribution, but with larger magnitudes for TFE. Also, would it be necessary to couple different thermostats to ethanol and trifluoroethanol in mixtures from x=0 to x=1? Certainly not. See http://www.gromacs.org/Documentation/Terminology/Thermostats Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011. For all questions about CloudBroker, please contact the company under i...@cloudbroker.com. In case you have any issues with the CloudBroker Platform, please send an email to our helpdesk at platf...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt Associate and Chair of the Management CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: i...@cloudbroker.com Web:http://www.cloudbroker.com -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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