[gmx-users] POSITION RESTRAIN ERROR
Dear Users, I am running Protein-Ligand MD simulations. Whenever, i get to do the Position restrain run of both my protein and ligand, i get this error; Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps. step 0 Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.080448, max 2.357673 (between atoms 2458 and 2457) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2458 2457 87.80.1141 0.3828 0.1140 2459 2458 86.70.1431 0.3658 0.1430 2461 2459 53.20.1340 0.1619 0.1340 2460 2459 53.20.1341 0.1672 0.1340 Wrote pdb files with previous and current coordinates Step 9, time 0.018 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 3.823957, max 98.964455 (between atoms 2458 and 2457) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2458 2457 78.00.3828 11.3959 0.1140 2459 2458 101.20.3658 10.0612 0.1430 2461 2459 85.50.1619 2.9966 0.1340 2460 2459 119.10.1672 4.7966 0.1340 2466 2460 141.30.1532 3.1407 0.1340 2467 2474 120.00.1132 0.6682 0.1120 2476 2474 39.00.1343 0.1077 0.1340 2467 2468 108.00.1483 0.7201 0.1470 2469 2468 33.90.1532 0.1473 0.1530 2464 2466 114.50.1455 0.5169 0.1390 2464 2465 44.60.1895 0.2021 0.1870 2462 2461 112.90.1640 5.8194 0.1400 2464 2462 87.10.1438 2.1170 0.1390 2463 2462 43.80.1125 1.2153 0.1090 Step 9, time 0.018 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.650577, max 22.438158 (between atoms 2466 and 2460) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2466 2464 114.50.1455 0.5169 0.1390 2465 2464 44.60.1895 0.2021 0.1870 2464 2462 87.10.1438 2.1170 0.1390 2462 2463 43.80.1125 1.2153 0.1090 2462 2461 112.90.1640 5.8194 0.1400 2459 2461 85.50.1619 2.9966 0.1340 2459 2460 119.10.1672 4.7966 0.1340 2459 2458 101.20.3658 10.0612 0.1430 2458 2457 78.00.3828 11.3959 0.1140 2466 2460 141.30.1532 3.1407 0.1340 2474 2467 120.00.1132 0.6680 0.1120 2468 2467 108.00.1483 0.7200 0.1470 2469 2468 33.90.1532 0.1473 0.1530 2476 2474 39.40.1343 0.1089 0.1340 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 2457 and 2460 at distance 14.992 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 Will be glad to learn how to go about it? Kind regards -- 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] POSITION RESTRAIN ERROR
On 9/25/13 6:05 AM, MUSYOKA THOMMAS wrote: Dear Users, I am running Protein-Ligand MD simulations. Whenever, i get to do the Position restrain run of both my protein and ligand, i get this error; Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps. step 0 Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.080448, max 2.357673 (between atoms 2458 and 2457) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2458 2457 87.80.1141 0.3828 0.1140 2459 2458 86.70.1431 0.3658 0.1430 2461 2459 53.20.1340 0.1619 0.1340 2460 2459 53.20.1341 0.1672 0.1340 Wrote pdb files with previous and current coordinates Step 9, time 0.018 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 3.823957, max 98.964455 (between atoms 2458 and 2457) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2458 2457 78.00.3828 11.3959 0.1140 2459 2458 101.20.3658 10.0612 0.1430 2461 2459 85.50.1619 2.9966 0.1340 2460 2459 119.10.1672 4.7966 0.1340 2466 2460 141.30.1532 3.1407 0.1340 2467 2474 120.00.1132 0.6682 0.1120 2476 2474 39.00.1343 0.1077 0.1340 2467 2468 108.00.1483 0.7201 0.1470 2469 2468 33.90.1532 0.1473 0.1530 2464 2466 114.50.1455 0.5169 0.1390 2464 2465 44.60.1895 0.2021 0.1870 2462 2461 112.90.1640 5.8194 0.1400 2464 2462 87.10.1438 2.1170 0.1390 2463 2462 43.80.1125 1.2153 0.1090 Step 9, time 0.018 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.650577, max 22.438158 (between atoms 2466 and 2460) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2466 2464 114.50.1455 0.5169 0.1390 2465 2464 44.60.1895 0.2021 0.1870 2464 2462 87.10.1438 2.1170 0.1390 2462 2463 43.80.1125 1.2153 0.1090 2462 2461 112.90.1640 5.8194 0.1400 2459 2461 85.50.1619 2.9966 0.1340 2459 2460 119.10.1672 4.7966 0.1340 2459 2458 101.20.3658 10.0612 0.1430 2458 2457 78.00.3828 11.3959 0.1140 2466 2460 141.30.1532 3.1407 0.1340 2474 2467 120.00.1132 0.6680 0.1120 2468 2467 108.00.1483 0.7200 0.1470 2469 2468 33.90.1532 0.1473 0.1530 2476 2474 39.40.1343 0.1089 0.1340 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 2457 and 2460 at distance 14.992 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 Will be glad to learn how to go about it? http://www.gromacs.org/Documentation/Terminology/Blowing_Up Without a description of your system, the .mdp file for the crashing run, and a full accounting of what you have done to prepare the system (EM, prior equilibration, etc) there is little point in speculating beyond saying that typically crashes are caused by bad .mdp settings or a flawed topology. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] position restrain dynamics error
Dear Sir, I am succesfully run molecules upto energy minimization, in case of position restrain md step , i have following, could you help to overcome the A charge group moved too far between two domain decomposition steps. Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.021061, max 0.387149 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.0960 0.1332 0.0960 Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.034712, max 0.636602 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.10.1332 0.1571 0.0960 Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1# Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1# Wrote pdb files with previous and current coordinates Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.023755, max 0.423951 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.1571 0.1367 0.0960 Step 4, time 0.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051081, max 0.931870 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.30.1367 0.1855 0.0960 Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1# Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1# Wrote pdb files with previous and current coordinates Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.020335, max 0.372790 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 89.90.1855 0.1318 0.0960 Step 6, time 0.012 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.056021, max 1.029913 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.20.1318 0.1949 0.0960 Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2# Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2# Wrote pdb files with previous and current coordinates Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.024586, max 0.451876 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.1949 0.1394 0.0960 with regards S. Boopathi -- 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] position restrain dynamics error
On 5/8/13 3:07 AM, Subramaniam Boopathi wrote: Dear Sir, I am succesfully run molecules upto energy minimization, in case of position restrain md step , i have following, could you help to overcome the A charge group moved too far between two domain decomposition steps. Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.021061, max 0.387149 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.0960 0.1332 0.0960 Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.034712, max 0.636602 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.10.1332 0.1571 0.0960 Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1# Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1# Wrote pdb files with previous and current coordinates Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.023755, max 0.423951 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.1571 0.1367 0.0960 Step 4, time 0.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051081, max 0.931870 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.30.1367 0.1855 0.0960 Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1# Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1# Wrote pdb files with previous and current coordinates Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.020335, max 0.372790 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 89.90.1855 0.1318 0.0960 Step 6, time 0.012 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.056021, max 1.029913 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.20.1318 0.1949 0.0960 Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2# Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2# Wrote pdb files with previous and current coordinates Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.024586, max 0.451876 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.1949 0.1394 0.0960 http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] position restrain of DNA
On 2/22/13 4:37 AM, Mehdi Bagherpour wrote: Tanks Justin Should I use from 'define = -DPOSRES' in mdp file? Use whatever #ifdef construct makes sense. The -DPOSRES uses the default posre.itp written by pdb2gmx, which restrains all heavy atoms. Unless you've modified the topology, that approach will not use your special restraint file. -Justin On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/21/13 7:35 PM, Mehdi Bagherpour wrote: Thanks Justin I have any question? i will use minimization with this restrain. using genrestr I make min.itp. how should I use this .itp file in grompp or mdrun? As you would any other .itp file; #include it in the topology, within the corresponding [moleculetype]. -Justin On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: I am using Gromacs software for DNA simulation. Specially in my project I need to fix two ends base pairs of DNA,The DNA that I want to simulate has 12 sequence shown bellow 5-- *C*GCAACG*C* --3 3-- *G*CGTTGC*G* --5 I dont know how I can use from position restraint in gromacs. would you please help me to solve this problem? Use genrestr with an index group specifying whatever it is that you want to restrain. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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] position restrain
Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073 15.0350 2 CH2 1 DRG CAH 20.115 14.0270 3 CH2 1 DRG CAI 30.367 14.0270 4NL 1 DRG N 4 -0.448 14.0067 5 H 1 DRG H1 50.346 1.0080 6 H 1 DRG H2 60.367 1.0080 7 CH1 1 DRG CA 70.297 13.0190 8 CH3 1 DRG CB 80.000 15.0350 9 C 1 DRG C 90.743 12.0110 10 O 1 DRG O10 -0.598 15.9994 11 N 1 DRG NAK11 -0.776 14.0067 12 H 1 DRG HAK120.400 1.0080 13 C 1 DRG CAP130.470 12.0110 14 CR1 1 DRG CAG140.157 12.0110 15 CH3 1 DRG CAL15 -0.072 1.0080 16 CR1 1 DRG CAF16 -0.309 12.0110 17HC 1 DRG HB4170.253 1.0080 18 S 1 DRG SAM180.089 32.0600 19 C 1 DRG CAQ19 -0.508 12.0110 20 C 1 DRG CAN200.968 12.0110 21 O 1 DRG OAD21 -0.619 15.9994 22OA 1 DRG OAL22 -0.347 15.9994 23 CH3 1 DRG CAB230.178 15.0350 and I have added 12 drugs in bilayer + sol and ion: [ molecules ] ; Compound#mols DRG 12 DMPC128 SOL 1943 CL 12 At the NVT step: I have to use position restrain for 12 drug molecules which I have added in bilayer, so I applied genrestr to make drg_posres.itp genrestr -f lip_12drg_solv_ion_em.gro -o drg_posre.itp -fc 1000 1000 1000 and I modified end of topology: ; Include Position restraint file #ifdef POSRES_DRG #include drg_posre.itp #endif ; Include DMPC chain topology #include dmpc.itp ; Include water topology #include gromos43a1_lipid.ff/spc.itp ; Include Position restraint file #ifdef POSRES_DRG #include drg_posre.itp #endif #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1_lipid.ff/ions.itp [ system ] ; Name drug in bilayer in water [ molecules ] ; Compound#mols DRG 12 DMPC128 SOL 1943 CL 12 when: grompp -f NVT.mdp -c lip_12_ion_em.gro -p topol_drg.top -o nvt.tpr Fatal error: [ file drg_posre.itp, line 28 ]: Atom index (24) in position_restraints out of bounds (1-23). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. please guide me if its possile. Thanks in advance. P.Haghighi -- 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] position restrain
Justin A. Lemkul wrote: parto haghighi wrote: Dear GMX users, I am working on lipid_drg system my drug molecule has 23 atoms. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.073 15.0350 2 CH2 1 DRG CAH 20.115 14.0270 3 CH2 1 DRG CAI 30.367 14.0270 4NL 1 DRG N 4 -0.448 14.0067 5 H 1 DRG H1 50.346 1.0080 6 H 1 DRG H2 60.367 1.0080 7 CH1 1 DRG CA 70.297 13.0190 8 CH3 1 DRG CB 80.000 15.0350 9 C 1 DRG C 90.743 12.0110 10 O 1 DRG O10 -0.598 15.9994 11 N 1 DRG NAK11 -0.776 14.0067 12 H 1 DRG HAK120.400 1.0080 13 C 1 DRG CAP130.470 12.0110 14 CR1 1 DRG CAG140.157 12.0110 15 CH3 1 DRG CAL15 -0.072 1.0080 16 CR1 1 DRG CAF16 -0.309 12.0110 17HC 1 DRG HB4170.253 1.0080 18 S 1 DRG SAM180.089 32.0600 19 C 1 DRG CAQ19 -0.508 12.0110 20 C 1 DRG CAN200.968 12.0110 21 O 1 DRG OAD21 -0.619 15.9994 22OA 1 DRG OAL22 -0.347 15.9994 23 CH3 1 DRG CAB230.178 15.0350 Side note - this topology does not appear to be sufficiently correct for use with 43A1. The charges are all odd values and the charge groups are not set correctly. I suspect you should spend some time doing significant reparameterization before doing any real simulations, otherwise you may spend a large amount of time to end up with junk. -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] position restrain file
Hi all, Does anyone know how to mannually make a position restrain file? There is a protein and a dendrimer in my system. And I want the protein to be the reference group. Thank you in advance. Xiuping -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] position restrain file
Ping wrote: Hi all, Does anyone know how to mannually make a position restrain file? There is a protein and a dendrimer in my system. And I want the protein to be the reference group. http://www.gromacs.org/Documentation/Gromacs_Utilities/genrestr -Justin Thank you in advance. Xiuping -- 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/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/mailing_lists/users.php
[gmx-users] Position Restrain
Dear all, I am trying to put a chain of polyleucine in water - hexane interface. Now after putting the chain of the peptide there are some overlaps. To get rid of those overlaps I tried to run a MD with the position of polyleucine constant (or restrained). But during energy minimization the polyleucine is coming out of the interface. I generated the posre.itp file with genrestr command and defined position restrain in the en.mdp file. My en.mdp file is as follows... cpp = /lib/cpp ;include = -I posre.itp define = -DPOSRES ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.001 nsteps = 1 ; ENERGY MINIMIZATION OPTIONS = emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 and also posre.itp is included in the topology as follows ; Include Position restraint file #ifdef POSRES #include posre.itp #endif I dont want the polyleucine to come out of the interface. Please help. Happy New Year to you all. Prithvi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Position Restrain
pandeyprithvi...@gmail.com wrote: Dear all, I am trying to put a chain of polyleucine in water - hexane interface. Now after putting the chain of the peptide there are some overlaps. To get rid of those overlaps I tried to run a MD with the position of polyleucine constant (or restrained). But during energy minimization the polyleucine is coming out of the interface. I generated the posre.itp file with genrestr command and defined position restrain in the en.mdp file. My en.mdp file is as follows... You are almost certainly seeing an artefact of periodic boundary conditions. If not, please describe your observations more fully (e.g. pictures) - coming out of the interface is quite vague. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark cpp = /lib/cpp ;include = -I posre.itp define = -DPOSRES ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.001 nsteps = 1 ; ENERGY MINIMIZATION OPTIONS = emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 and also posre.itp is included in the topology as follows ; Include Position restraint file #ifdef POSRES #include posre.itp #endif I dont want the polyleucine to come out of the interface. Please help. Happy New Year to you all. Prithvi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Position Restrain md
Hi, How can I make sure that position restraint is actually applied (after grompp mdrun)? When I grep POSRES or posres I can not see any information... Many Thanks in Advance/Jamie On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let me know what I am missing here?? Many Thanks in Advance/Jamie pdb2gmx automatically produces a posre.itp file, whose position restraint contents are #included from the .top file it produces, and whose function is sensitive to the -DPOSRES option. Search the wiki for discussion of this machinery. Mark On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? It includes the whole system, but it is often a good idea not to couple groups of heterogeneous heat capacity to the same thermostat. That said, if the groups are too small, you get other problems. See also http://oldwiki.gromacs.org/index.php/temperature_coupling (2) In this case how program recognize which one should restrain and which one not, because it included all?? Temperature coupling has no linkage with position restraints. You defined the latter in your .top file. (3) This step is required for every system or only proteins?? It may or may not be useful in achieving stable equilibration for any system. See http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? constraints are different from restraints in GROMACS usage. make_ndx does allow you to generate new index groups, but you will need to (re-)read the relevant manual sections to understand that neither of these algorithms uses index groups. (Or to prove my memory wrong!) (5) In my case I have a molecule (MOL) and water (SOL), for position restrain md should I use tc_grps=MOL SOL (according to fws tutorial) or I need only write tc_grps=MOL?? Many Thanks in Advance/Jamie The latter won't work, for all atoms must be members of a temperature-coupling group if any are. What you actually need is a clear understanding of your strategic objective. Hopefully some of the links will move you towards that. 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Position Restrain md
Hi Justin, Thanks for your complete answer. Actually I have another question here. It is about potential energy after mdrun. From md.log in AVERAGES section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the same order. Can I trust these results or I did something wrong? Is it always the same order for different systems? Can you please give me some advice about it?? Many Thanks in Advance/ Jamie On Sat, Aug 15, 2009 at 6:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jamie Seyed wrote: Hi, How can I make sure that position restraint is actually applied (after grompp mdrun)? When I grep POSRES or posres I can not see any information... Many Thanks in Advance/Jamie If your topology has the appropriate #ifdef POSRES, and you have define = -DPOSRES in your .mdp file, then it worked :) Position restraints are applied during mdrun, and show up in the .log file as Position Rest. entries. -Justin On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let me know what I am missing here?? Many Thanks in Advance/Jamie pdb2gmx automatically produces a posre.itp file, whose position restraint contents are #included from the .top file it produces, and whose function is sensitive to the -DPOSRES option. Search the wiki for discussion of this machinery. Mark On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? It includes the whole system, but it is often a good idea not to couple groups of heterogeneous heat capacity to the same thermostat. That said, if the groups are too small, you get other problems. See also http://oldwiki.gromacs.org/index.php/temperature_coupling (2) In this case how program recognize which one should restrain and which one not, because it included all?? Temperature coupling has no linkage with position restraints. You defined the latter in your .top file. (3) This step is required for every system or only proteins?? It may or may not be useful in achieving stable equilibration for any system. See http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? constraints are different from restraints in GROMACS usage. make_ndx does allow you to generate new index groups, but you will need to (re-)read the relevant manual sections to understand that neither of these algorithms uses index groups. (Or to prove my memory wrong!) (5) In my case I have a molecule (MOL) and water (SOL), for position restrain md should I use tc_grps=MOL SOL (according to fws tutorial) or I need only write tc_grps=MOL?? Many Thanks in Advance/Jamie The latter won't work, for all atoms must be members of a temperature-coupling group if any are. What you actually need is a clear understanding of your strategic objective. Hopefully some of the links will move you towards that. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
Re: [gmx-users] Position Restrain md
Jamie Seyed wrote: Hi Justin, Thanks for your complete answer. Actually I have another question here. It is about potential energy after mdrun. From md.log in AVERAGES section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the same order. Can I trust these results or I did something wrong? Is it always the same order for different systems? Can you please give me some advice about it?? Many Thanks in Advance/ Jamie I don't know anything about your system, so it's hard to make a generalization. Positive values of potential indicate repulsive or unsatisfied interactions. If you're running your system in solvent, I would think something is wrong; vacuum might be a different story, but I don't usually do vacuum simulations, so I don't have any real expertise here. -Justin On Sat, Aug 15, 2009 at 6:37 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jamie Seyed wrote: Hi, How can I make sure that position restraint is actually applied (after grompp mdrun)? When I grep POSRES or posres I can not see any information... Many Thanks in Advance/Jamie If your topology has the appropriate #ifdef POSRES, and you have define = -DPOSRES in your .mdp file, then it worked :) Position restraints are applied during mdrun, and show up in the .log file as Position Rest. entries. -Justin On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let me know what I am missing here?? Many Thanks in Advance/Jamie pdb2gmx automatically produces a posre.itp file, whose position restraint contents are #included from the .top file it produces, and whose function is sensitive to the -DPOSRES option. Search the wiki for discussion of this machinery. Mark On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? It includes the whole system, but it is often a good idea not to couple groups of heterogeneous heat capacity to the same thermostat. That said, if the groups are too small, you get other problems. See also http://oldwiki.gromacs.org/index.php/temperature_coupling (2) In this case how program recognize which one should restrain and which one not, because it included all?? Temperature coupling has no linkage with position restraints. You defined the latter in your .top file. (3) This step is required for every system or only proteins?? It may or may not be useful in achieving stable equilibration for any system. See http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? constraints are different from restraints in GROMACS usage. make_ndx
[gmx-users] Position Restrain md
Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? (2) In this case how program recognize which one should restrain and which one not, because it included all?? (3) This step is required for every system or only proteins?? (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? (5) In my case I have a molecule (MOL) and water (SOL), for position restrain md should I use tc_grps=MOL SOL (according to fws tutorial) or I need only write tc_grps=MOL?? Many Thanks in Advance/Jamie ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Position Restrain md
Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? It includes the whole system, but it is often a good idea not to couple groups of heterogeneous heat capacity to the same thermostat. That said, if the groups are too small, you get other problems. See also http://oldwiki.gromacs.org/index.php/temperature_coupling (2) In this case how program recognize which one should restrain and which one not, because it included all?? Temperature coupling has no linkage with position restraints. You defined the latter in your .top file. (3) This step is required for every system or only proteins?? It may or may not be useful in achieving stable equilibration for any system. See http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? constraints are different from restraints in GROMACS usage. make_ndx does allow you to generate new index groups, but you will need to (re-)read the relevant manual sections to understand that neither of these algorithms uses index groups. (Or to prove my memory wrong!) (5) In my case I have a molecule (MOL) and water (SOL), for position restrain md should I use tc_grps=MOL SOL (according to fws tutorial) or I need only write tc_grps=MOL?? Many Thanks in Advance/Jamie The latter won't work, for all atoms must be members of a temperature-coupling group if any are. What you actually need is a clear understanding of your strategic objective. Hopefully some of the links will move you towards that. 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/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/mailing_lists/users.php
Re: [gmx-users] Position Restrain md
Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let me know what I am missing here?? Many Thanks in Advance/Jamie On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? It includes the whole system, but it is often a good idea not to couple groups of heterogeneous heat capacity to the same thermostat. That said, if the groups are too small, you get other problems. See also http://oldwiki.gromacs.org/index.php/temperature_coupling (2) In this case how program recognize which one should restrain and which one not, because it included all?? Temperature coupling has no linkage with position restraints. You defined the latter in your .top file. (3) This step is required for every system or only proteins?? It may or may not be useful in achieving stable equilibration for any system. See http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? constraints are different from restraints in GROMACS usage. make_ndx does allow you to generate new index groups, but you will need to (re-)read the relevant manual sections to understand that neither of these algorithms uses index groups. (Or to prove my memory wrong!) (5) In my case I have a molecule (MOL) and water (SOL), for position restrain md should I use tc_grps=MOL SOL (according to fws tutorial) or I need only write tc_grps=MOL?? Many Thanks in Advance/Jamie The latter won't work, for all atoms must be members of a temperature-coupling group if any are. What you actually need is a clear understanding of your strategic objective. Hopefully some of the links will move you towards that. 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Position Restrain md
Jamie Seyed wrote: Hi Mark, Thanks for the answers. One question still remains for me: in the fws tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run grompp followed by mdrun... Am I missing some thing? Because I can not see it introduces something that to be restrained..?? Would you please let me know what I am missing here?? Many Thanks in Advance/Jamie pdb2gmx automatically produces a posre.itp file, whose position restraint contents are #included from the .top file it produces, and whose function is sensitive to the -DPOSRES option. Search the wiki for discussion of this machinery. Mark On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Jamie Seyed wrote: Dear all, I have questions regarding the position restrain md. I tried to find the answer of my questions from the mailing list, but it is not clear yet. In the fws tutorial when it says (in the pr.mdp) tc_grps=Protein non-protein (1) Doesn't that mean everything in the system? I think for this case we can simply write system because system is made by protein and non-protein?? It includes the whole system, but it is often a good idea not to couple groups of heterogeneous heat capacity to the same thermostat. That said, if the groups are too small, you get other problems. See also http://oldwiki.gromacs.org/index.php/temperature_coupling (2) In this case how program recognize which one should restrain and which one not, because it included all?? Temperature coupling has no linkage with position restraints. You defined the latter in your .top file. (3) This step is required for every system or only proteins?? It may or may not be useful in achieving stable equilibration for any system. See http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation (4) If I want to make an index file and I specify a group that need to be constrained, in the generated index file I will get system and all its parts and an extra part for my specific part that need to be constrain...Is that ok?? constraints are different from restraints in GROMACS usage. make_ndx does allow you to generate new index groups, but you will need to (re-)read the relevant manual sections to understand that neither of these algorithms uses index groups. (Or to prove my memory wrong!) (5) In my case I have a molecule (MOL) and water (SOL), for position restrain md should I use tc_grps=MOL SOL (according to fws tutorial) or I need only write tc_grps=MOL?? Many Thanks in Advance/Jamie The latter won't work, for all atoms must be members of a temperature-coupling group if any are. What you actually need is a clear understanding of your strategic objective. Hopefully some of the links will move you towards that. 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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] POSITION-RESTRAIN
Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] POSITION-RESTRAIN
Morteza Khabiri wrote: Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? You're using a [ position_restraints ] directive that requires at least 53 atoms in a position where only 52 are defined. There are various explanations, including #including in the wrong place, or #including a wrong file. Look carefully at a correct example. 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/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/mailing_lists/users.php
Re: [gmx-users] POSITION-RESTRAIN
--- On Mon, 27/7/09, Morteza Khabiri khab...@greentech.cz wrote: From: Morteza Khabiri khab...@greentech.cz Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users@gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? Thanks hi, Mark is right.the position restrain.itp file should be included in your topology file in the proper place otherwise the problem would continue. place the .itp file after the section ; Include Position restraint file #ifdef POSRES #include posre.itp #endif best wishes Shamik ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.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/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/mailing_lists/users.php
[gmx-users] POSITION-RESTRAIN
Sounds to me like you have a 52 atom lipid and have a posre.itp file with more than 52 atoms (or referencing atom numbers greater than 52). What one usually does is has a somelipid.itp file that, upon some .mdp define, includes a someposre.itp file that looks like this: [ position_restraints ] ; atom type fx fy fz 8 1 1000 1000 1000 where for a 52 atom lipid I assume that you are using Berger lipids and atom 8 is the Phosphorous. On the other hand, if you have a .itp file that specifies N-lipids, then you would need lots of [ position_restraints ]. Caution: this is not the best way to go as you will need to modify many files every time you set up a new bilayer. As an analogy, look at the way that the SOL (tip4p in this case) posre is applied in a generic .top out of pdb2gmx: #include tip4p.itp #ifdef POSRES_SOL ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif where it is a per-molecule atomic index definition such that atom 1 is applied to each solvent molecule. If you are still unclear, I strongly suspect that there is a gmx manual description of all of this, and suggest that you read the manual in search of it. If you can't find one then probably you should complain back to this list about the absence of a section that should definitely be there. Chris. -- original message -- From: Morteza Khabiri khabiri at greentech.cz Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users at gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? Thanks hi, Mark is right.the position restrain.itp file should be included in your topology file in the proper place otherwise the problem would continue. place the .itp file after the section ; Include Position restraint file #ifdef POSRES #include posre.itp #endif best wishes Shamik ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times
Creighton Buie wrote: Hello Gromacs Community, I am trying to set up a system where there is a coarse grained hydrophobic polymer floor in a solvated water box. I am using the martini force field with an .itp file for the polymer. The floor is basically the polymer spaced 0.5 nm apart from each other and the bottom bead is fixed in the X, Y, and Z direction. I have tried many ways of fixing this bead using both freeze groups and position restrained techniques, both to no avail. I am using PME and no part of the system has a charge. The latest try has consisted of using the position restrain line in the .itp file of the polymer through the topology file and fixing the bottom bead with a force of 1000 in X Y Z. The energy minimization run went smoothly but when I try to do any type of md I get this error message: Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of432 missing 1 --- Program mdrun, VERSION 4.0.3 Source code file: domdec_top.c, line: 172 Software inconsistency error: Some interactions seem to be assigned multiple times --- You Can Always Go On Ricky Lake (Offspring) After searching the mailing list about this error I could only find that it was a bug. Is this correct? Any suggestions is much appreciated. If so, you should try an up-to-date version of GROMACS - 4.0.4 is current. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] position restrain
Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] position restrain
shahrbanoo karbalaee wrote: Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? pcoupl = yes doesn't do anything. You have to specify the type of pressure coupling (grompp should tell you that). For a discussion of the differences of NVT and NPT (and statistical ensembles in general), do some background reading on statistical mechanics and thermodynamics. It is hard to say ad hoc whether or not NPT conditions will change your data. -Justin best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Re: [gmx-users] Position restrain of protein and membrane
Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing). So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions). You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection. -Justin Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www
[gmx-users] Position restrain of protein and membrane
Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? No. If your lipids are just a 'solvent', then treat them as you would treat water. If you are specifically interested in the lipid conformations and dynamics then treat them as you would treat water if you were interested in the specific solvation and dynamic properties of water. Lipid bilayers are essentially a bulk system, the same as water, but different from an embedded protein. Personally, I do 5 ns posre on the protein after insertion and then it takes 15+ ns for general protein equilibration. This is from the make-hole version of gmx 3.1.4, which I consider to be optimal for reducing equilibration time, so your required equilibration time may be greater... check time-dependent RMSDs. On a slightly separate note, I know that many papers do not give a full methods description, but many also do. If you have indeed read many membrane protein simulation papers and it is your intention to question if it is an absolute truth that lipids need not be position restrained during equilibration then that is something that you would need to elucidate yourself as I have not seen that studied explicitly (although I highly doubt that this is the case). Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Re: [gmx-users] Position restrain of protein and membrane
Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing). So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions). You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection. -Justin Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] Position restrain of protein and membrane
minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: Re: [gmx-users] Position restrain of protein and membrane
Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Position restrain of protein and membrane
minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing). So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions). You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection. -Justin Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the
Re: Re: [gmx-users] Position restrain of protein and membrane
Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] position restrain
Thanks for your help. My simulation ran with your idea. Date: Thu, 15 Nov 2007 13:34:40 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] position restrain If you read the documentation for genpr, it tells you that it will only generate a position restraint file for the first molecule, so grompp is telling you that only the protein is being restrained, which is what you should expect. If you really insist on restraining the water molecules, try reading about the freezegrps options for your .mdp file, but doing so will typically cause problems if you are using pressure coupling. -Justin Quoting pragya chohan [EMAIL PROTECTED]: hi I have a system of protein, popc,water and Cl ions. I want to position restrain protein and water as without position restrain water is going into the membrane . So I made a group of protein and water together using make_ndx and then genpr. When i ran grompp i got the following error: --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1108 Fatal error: [ file posre1.itp, line 582 ]: Atom index (5362) in position_restraints out of bounds (1-577) The commands i used are: make_ndx -f em_dpt_popc.gro -o 0 System : 12663 atoms 1 Protein : 577 atoms 2 Protein-H : 456 atoms 3 C-alpha :59 atoms 4 Backbone: 177 atoms 5 MainChain : 237 atoms 6 MainChain+Cb: 294 atoms 7 MainChain+H : 296 atoms 8 SideChain : 281 atoms 9 SideChain-H : 219 atoms 10 Prot-Masses : 577 atoms 11 Non-Protein : 12086 atoms 12 POPC: 4784 atoms 13 SOL : 7299 atoms 14 Cl : 3 atoms 15 Other : 12086 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 1|13 Copied index group 1 'Protein' Copied index group 13 'SOL' Merged two groups with OR: 577 7299 - 7876 16 Protein_SOL : 7876 atoms q genpr -f em_dpt_popc.gro -o posre1 -n index.ndx Group16 ( Protein_SOL) has 7876 elements Select a group: 16 Selected 16: 'Protein_SOL' grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o pr_dpt_popc What is the best way to do this? Please suggest. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _ Get the new Windows Live Messenger! http://get.live.com/messenger/overview___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] position restrain
hi I have a system of protein, popc,water and Cl ions. I want to position restrain protein and water as without position restrain water is going into the membrane . So I made a group of protein and water together using make_ndx and then genpr. When i ran grompp i got the following error: --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1108 Fatal error: [ file posre1.itp, line 582 ]: Atom index (5362) in position_restraints out of bounds (1-577) The commands i used are: make_ndx -f em_dpt_popc.gro -o 0 System : 12663 atoms 1 Protein : 577 atoms 2 Protein-H : 456 atoms 3 C-alpha :59 atoms 4 Backbone: 177 atoms 5 MainChain : 237 atoms 6 MainChain+Cb: 294 atoms 7 MainChain+H : 296 atoms 8 SideChain : 281 atoms 9 SideChain-H : 219 atoms 10 Prot-Masses : 577 atoms 11 Non-Protein : 12086 atoms 12 POPC: 4784 atoms 13 SOL : 7299 atoms 14 Cl : 3 atoms 15 Other : 12086 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 1|13 Copied index group 1 'Protein' Copied index group 13 'SOL' Merged two groups with OR: 577 7299 - 7876 16 Protein_SOL : 7876 atoms q genpr -f em_dpt_popc.gro -o posre1 -n index.ndx Group16 ( Protein_SOL) has 7876 elements Select a group: 16 Selected 16: 'Protein_SOL' grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o pr_dpt_popc What is the best way to do this? Please suggest. _ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] position restrain
If you read the documentation for genpr, it tells you that it will only generate a position restraint file for the first molecule, so grompp is telling you that only the protein is being restrained, which is what you should expect. If you really insist on restraining the water molecules, try reading about the freezegrps options for your .mdp file, but doing so will typically cause problems if you are using pressure coupling. -Justin Quoting pragya chohan [EMAIL PROTECTED]: hi I have a system of protein, popc,water and Cl ions. I want to position restrain protein and water as without position restrain water is going into the membrane . So I made a group of protein and water together using make_ndx and then genpr. When i ran grompp i got the following error: --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1108 Fatal error: [ file posre1.itp, line 582 ]: Atom index (5362) in position_restraints out of bounds (1-577) The commands i used are: make_ndx -f em_dpt_popc.gro -o 0 System : 12663 atoms 1 Protein : 577 atoms 2 Protein-H : 456 atoms 3 C-alpha :59 atoms 4 Backbone: 177 atoms 5 MainChain : 237 atoms 6 MainChain+Cb: 294 atoms 7 MainChain+H : 296 atoms 8 SideChain : 281 atoms 9 SideChain-H : 219 atoms 10 Prot-Masses : 577 atoms 11 Non-Protein : 12086 atoms 12 POPC: 4784 atoms 13 SOL : 7299 atoms 14 Cl : 3 atoms 15 Other : 12086 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 1|13 Copied index group 1 'Protein' Copied index group 13 'SOL' Merged two groups with OR: 577 7299 - 7876 16 Protein_SOL : 7876 atoms q genpr -f em_dpt_popc.gro -o posre1 -n index.ndx Group16 ( Protein_SOL) has 7876 elements Select a group: 16 Selected 16: 'Protein_SOL' grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o pr_dpt_popc What is the best way to do this? Please suggest. _ Check out some new online services at Windows Live Ideasso new they havent even been officially released yet. http://www.msnspecials.in/windowslive/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Position restrain
It is all about order.
You have to include the position restraint .itp directly after the
molecule .itp (or inside the molecule.itp).
If you place it behind the solvent .itp it will assume the position
restraints refers to the solvent.
The atom numbers in the position restraint should match the atom
numbers in the relevant molecule.itp
--- Alessandro Mattozzi [EMAIL PROTECTED] wrote:
mh, actually the status is like this: my system is made of two kind
of molecules: one (solvent) with 12 atoms and the other with more
(thousands); i tried to run only with the big molecule and it works
perfectly, it means the atoms restrained are those according to the
index number;
when i introduce the molecule of solvent, it looks like I can lock
only the solvent; how can I specify in the grompp the the position
restrain refers to on .itp (the molecule) and not the solvent .itp? I
thought that using atom index from the gro file would have worked
Thanks a lot!
Regards
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
-Original Message-
From: [EMAIL PROTECTED] on behalf of Uwe Richter
Sent: Thu 6/1/2006 11:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position restrain
Hi,
concept of 'molecules' as it is applied within Gromacs has been
discussed
several times already, also with regards to distance restraints,
which can
not be defined between different 'molecules'. Of course you can
define
distance restraints between 'real' molecules by having the molecules
within the same topology block (atoms,bonds etc.), just without any
bonding parameters defined between them. Position restraints also
have
to be defined for each topology block ('molecule') and are read in
this
way by grompp. The index file .ndx referres to the atom numbering in
the
structure file (.pdb .gro ...). The id's of the position restraints,
however,
refer to atom numbering within the 'molecule', starting from 1 for
each, and
thus ,must be defined/included right after the corresponding
'molecule'
in the
.top file.
This is a little confusing and my chaotic description might not help
a lot,
but it seems you have more than one 'molecule' in your system and the
one you want the position restraints for only has 12 atoms, even
though it
might have the atom id 101 in your coordinate file.
Best regards,
Uwe
Alessandro Mattozzi wrote:
While running a MD of PE with position restrain, i get this error
message
Fatal error: [ file posre.itp, line 6 ]:
Atom index (101) in position_restraints out of bounds
(1-12)
My atom index goes up to 6000, why do I have to be in the 1-12
range?
your molecule only has 12 atoms and by the way, the error message
is
from grompp.
actually my molecule has 12 thousand atoms, half of it dummies and
half AUA. The .gro and .ndx contains atoms numbered up to 12000
The error ideed comes from grompp.
Thanx
Regards
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
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RE: [gmx-users] Position restrain
While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? your molecule only has 12 atoms and by the way, the error message is from grompp. actually my molecule has 12 thousand atoms, half of it dummies and half AUA. The .gro and .ndx contains atoms numbered up to 12000 The error ideed comes from grompp. Thanx Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] Position restrain
Hi,
concept of 'molecules' as it is applied within Gromacs has been discussed
several times already, also with regards to distance restraints, which can
not be defined between different 'molecules'. Of course you can define
distance restraints between 'real' molecules by having the molecules
within the same topology block (atoms,bonds etc.), just without any
bonding parameters defined between them. Position restraints also have
to be defined for each topology block ('molecule') and are read in this
way by grompp. The index file .ndx referres to the atom numbering in the
structure file (.pdb .gro ...). The id's of the position restraints,
however,
refer to atom numbering within the 'molecule', starting from 1 for each, and
thus ,must be defined/included right after the corresponding 'molecule'
in the
.top file.
This is a little confusing and my chaotic description might not help a lot,
but it seems you have more than one 'molecule' in your system and the
one you want the position restraints for only has 12 atoms, even though it
might have the atom id 101 in your coordinate file.
Best regards,
Uwe
Alessandro Mattozzi wrote:
While running a MD of PE with position restrain, i get this error message
Fatal error: [ file posre.itp, line 6 ]:
Atom index (101) in position_restraints out of bounds (1-12)
My atom index goes up to 6000, why do I have to be in the 1-12 range?
your molecule only has 12 atoms and by the way, the error message is
from grompp.
actually my molecule has 12 thousand atoms, half of it dummies and half AUA.
The .gro and .ndx contains atoms numbered up to 12000
The error ideed comes from grompp.
Thanx
Regards
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
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[gmx-users] Position restrain
Title: Position restrain While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] Position restrain
Alessandro Mattozzi wrote: While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? your molecule only has 12 atoms and by the way, the error message is from grompp. Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] Position restrain
Alessandro Mattozzi wrote: Hi How should my posres.itp look like? Is there any template available? Thank Regards genpr does generate position rstrains ... -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-page: http://md.chem.rug.nl/~periole -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
[gmx-users] Position restrain of protein and membrane
-> [gmx-users] Position restrain of protein and membrane gmx-users -- Thread -- -- Date -- <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Reply via email to <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FFFFFF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "000000"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Reply via email to <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale [gmx-users] Position restrain of protein and membrane chris . neale Reply via email to <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale [gmx-users] Position restrain of protein and membrane chris . neale Re: Re: [gmx-users] Position restrain of protein and membrane minnale Reply via email to
[gmx-users] Position restrain of protein and membrane
-> Re: [gmx-users] Position restrain of protein and membrane gmx-users -- Thread -- -- Date -- <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "000000"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Reply via email to <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FFFFFF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "000000"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Reply via email to <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale [gmx-users] Position restrain of protein and membrane chris . neale Reply via email to <!-- google_ad_client = "pub-7266757337600734"; google_alternate_ad_url = "http://www.mail-archive.com/blank.png"; google_ad_width = 160; google_ad_height = 600; google_ad_format = "160x600_as"; google_ad_channel = "8427791634"; google_color_border = "FF"; google_color_bg = "FF"; google_color_link = "006792"; google_color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale [gmx-users] Position restrain of protein and membrane chris . neale Re: Re: [gmx-users] Position restrain of protein and membrane minnale Reply via email to
