[gmx-users] Re: Requesting Help
Anirban, It is better to keep conversations on the gmx-user list where I believe you found much help already. I looked quickly at your EM.gro file. There several issues that you should have picked your self quite easily using VMD. 1- there are 3 empty line in your gro file: lines 204, 2253 and 4302. 2- when this fixed and the number of atoms in the second line of the file changed, I looked at the protein only and noticed very clearly that your conformation, although looking reasonable overall, has serious problems. This is clear when looking at the backbone only. Several portions of your protein have Calpha-Calpha distances that exceed a reasonable distance (0.42 nm). Note that in the MARTINI 2.1 version the distance is 0.35 nm. You can visualize them by uploading your corrected EM.gro in VMD and choosing a dynamicbonds representation on the following selected atoms: name BC*.* BH*.*, the missing atoms would appear by repeating this selection and showing them in CPK. I picked the following regions but it might be more: - residues 33-38 - 105-108 - 141-161 (this one is really funky) - 168-171 - 200-206 - 212-213 - 239-246 - 253-258 This is only where distances appear too long but all over the structure distances also appeared to short. In conclusion your protein structure is seriously damaged, this is probably not a problem of your protocol but your atomistic starting structure. You should check it and fix it before going further in the simulation. This should help. XAvier. On Nov 3, 2009, at 6:16 AM, Anirban wrote: Respected Sir, Thank you very much for the reply. Actually, packed the lipids around my protein using InflateGRO program and then solvated it using genbox. Then I ran EM which ran quite well. But still am getting that error. I am attaching my .gro file. If you find any time, please have a look at it and comment. Thank you once again. Regards, On Sat, 2009-10-31 at 10:49 +0100, XAvier Periole wrote: Dear Anirban, Your mdp file seems fine to me. If I were you I would look at the system. It probably contains bad contacts between different parts you put together, which makes it explode, if this is what happens (difficult to tell from the output message). I would also suggest that you contact the gmx-user list and search the archive. Someone might have had the same problem or might be able to help you. Best, XAvier. On Oct 30, 2009, at 4:13 PM, Anirban wrote: Respected Sir, I have gone through your paper on Rhodopsin self-assembly study. I am also trying a similar thing on the CGMD study of a GPCR protein in a lipid bilayer. I have using MARTINI FF and have successfully built my system. The EM ran well, but I am getting problem with MD run. I am attaching my mdp file. I am getting the following error in the very first step: Number of grid cells is zero. Probably the system and box collapsed. Please advice how to solve this issue. Regards, -- Anirban Ghosh Grade Based Engineer Bioinformatics Team Scientific Engineering Computing Group Centre for Development of Advanced Computing Pune, India -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. md.mdp -- Anirban Ghosh Grade Based Engineer Bioinformatics Team Scientific Engineering Computing Group Centre for Development of Advanced Computing Pune, India -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. EM.gro ___ 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] grompp
Hi I used grompp command but follow fatal error appeared: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. please guide me ___ 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] empty edr and trr file
Hi, I have LiCl solutions, SPCE and TIP4P2005 water models and OPLS. It worked for both models with one concentration, this one also works with SPCE, but using TIP4P2005 stops writing somehow. The program mdrun does not crash for a day even, seems to run, but the .edr and .trr files are empty, the .log file stops at last writing out step 0 or even earlier. I tried what I found on the list as suggestions on such problems: the problem of huge configuration (I have like 11000atoms) setting few steps and frequent output; using PME insetad of Ewald and I checked the input files as carefully as I could, also (they are basically the same ones used and run before - minimally modified, of course). I haven't found it in the debug files either (maybe I was not checking the right ones?) I tried grompp and mdrun also. I hope somebody has some idea, where should I see the mistake. Thank you for reading Ildiko ___ 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] grompp
-- Forwarded message -- From: leila karami karami.lei...@gmail.com Date: Tue, Nov 3, 2009 at 1:50 PM Subject: grompp To: gmx-users@gromacs.org Hi I used grompp command ( grompp -f -c o -p c -o t.tpr) but a mdout.mdp file is created and follow fatal error appeared: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. please guide me ___ 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] g_sas with pbc
Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using the command: trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box 7.3973 7.3973 7.3973 In the reference.pdb I've also the CRYST informations. I've modified the gmx_sas.c to bypass the check that turn off automatically the PBC if solvent molecules are not present. Unfortunately I've seen that the results with and without taking into account the PBC are identical. So my questions are: 1) Is it possible to use the g_sas tool to calculate the SAS of this kind of system? 2) There are some tricks or trasformations or missing informations in my input(s) that I could fill before running the analysis? 3)Should I use another type of box? Trasform the trajectory with some pbc keywords (I've also tried -ur compact without luck)... Thanks in advance and sorry for the long message Andrea ___ 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] g_sas with pbc
andrea carotti wrote: Hi all, I've already simulated 27 organic molecules in a cubic solvent box. Now I would like to calculate the SAS of this system. I've a tpr and a trr with only the molecules inside (without water). I'm using gromacs 4.0.5. I've added the box dimension infos to the trr using the command: trjconv -f ../../original_multi3000.pdb -o new.trr -s reference.pdb -box 7.3973 7.3973 7.3973 In the reference.pdb I've also the CRYST informations. I've modified the gmx_sas.c to bypass the check that turn off automatically the PBC if solvent molecules are not present. Unfortunately I've seen that the results with and without taking into account the PBC are identical. So my questions are: 1) Is it possible to use the g_sas tool to calculate the SAS of this kind of system? 2) There are some tricks or trasformations or missing informations in my input(s) that I could fill before running the analysis? 3)Should I use another type of box? Trasform the trajectory with some pbc keywords (I've also tried -ur compact without luck)... Thanks in advance and sorry for the long message Andrea There is an open bugzilla on this http://bugzilla.gromacs.org/show_bug.cgi?id=197 In principle it should work, but there may still be a small bug. Feel free to upload a test system to this bugzilla. ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ 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] grompp
leila karami wrote: Hi I used grompp command but follow fatal error appeared: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. please guide me http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds Beyond that, search the list archive; this comes up quite often when you've improperly formatted the topology. -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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] gmx user
Hello Users, I am trying to install gromacs on windows and find lot of problems. First I have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and configure it but when I used make and make install commands but some directories leave as it is. When configure gromacs-4.0.5 then it will shows error in configuration file line no 14 and 25 about $ '/r' command not found and syntax error. so please tell me the solution. -- Pawan Kumar Raghav ___ 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] grompp
dear justin I use amber force field in gromacs.can this subject make such error : Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. ___ 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] gmx user
pawan raghav wrote: Hello Users, I am trying to install gromacs on windows and find lot of problems. First I have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and configure it but when I used make and make install commands but some directories leave as it is. When configure gromacs-4.0.5 then it will shows error in configuration file line no 14 and 25 about $ '/r' command not found and syntax error. so please tell me the solution. Copying and pasting output from the terminal is more useful than this parsed interpretation of what is going on. If neither process fails with any errors, it was probably fine. Compiler warnings do sometimes arise, but again, in the absence of errors (which terminate compilation), you should be fine. If you want further information, post real output from the terminal. -Justin -- Pawan Kumar Raghav ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] grompp
leila karami wrote: dear justin I use amber force field in gromacs.can this subject make such error : Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. Did you read the solution I posted before? You have #included your water .itp file in the wrong place. -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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms
Hi everyone !! I am having a problem using pdb2gmx command. Using the command on my input pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms. I do not have only O either in input pdb file or in rtp file. and its O and not 0 (zero). My part of input files reads as ATOM 1 NCCMT 1 -2.521 -2.813 2.083 0.00 0.00 ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00 ATOM 3 CCCMT 1 -1.711 -0.842 0.859 0.00 0.00 ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00 ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00 ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00 ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00 ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00 ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00 ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00 ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00 ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00 ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00 ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00 ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00 ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00 ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00 ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00 ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00 ATOM 20 HCCMT 1 -1.801 -3.362 1.658 0.00 0.00 ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00 ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00 ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00 ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00 ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00 ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00 ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00 ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00 ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00 ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00 ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00 ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00 ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00 ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00 ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00 ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00 ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00 ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00 and my part of .rtp file is [ CCMT ] [ atoms ] Namber99_34 -0.3961651 Hamber99_17 0.2951872 CAamber99_11 -0.0735013 HAamber99_19 0.1405104 CBamber99_11 -0.2213715 HB1amber99_19 0.1465376 HB2amber99_19 0.1465377 SGamber99_48 -0.2851828 SDamber99_68 -0.089 ;SM CEamber99_69 -0.10 10 HE1amber99_70 -0.09 11 HE2amber99_70 -0.09 12 CZamber99_71 -0.003 13 CHamber99_73 0.334 14 CH1amber99_74 -0.337 15 HH11amber99_76 0.090 16 HH12amber99_76 0.090 17 HH13amber99_76 0.090 18 CH2amber99_74 -0.337 19 HH21amber99_76 0.090 20 HH22amber99_76 0.090 21 HH23amber99_76 0.090 22 NT1amber99_77 0.220 23 OT1amber99_78 -0.438 24 CIamber99_75 0.329 25 CI1amber99_74 -0.337 26 HI11amber99_76 0.090 27 HI12amber99_76 0.090 28 HI13amber99_76 0.090 29 CI2amber99_74 -0.337 30 HI21amber99_76 0.090 31 HI22amber99_76 0.090 32 HI23amber99_76 0.090 33 CKamber99_72 -0.340 34 HKamber99_79 0.162 35 Camber99_20.643035 36 OC1amber99_45 -0.7981037 OC2amber99_45 -0.7981038 Any help is heartly welcomed. Thanks in advance Chandan -- Chandan kumar Choudhury NCL, Pune INDIA ___ 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] grompp
dear justin Fatal error: [ file spc.itp, line 46 ]: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. I checked topology file and sent topology and spc.itp file. please guide me. this is my topology file : ; Include forcefield parameters #include ffamber03.itp ; Include chain topologies #include c_A.itp #include c_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL 7127 this is my spc.itp file: [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifdef _FF_GROMACS 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1SOL OW 1 -0.829.95140 2 H 1SOLHW1 1 0.414.03200 3 H 1SOLHW2 1 0.414.03200 #else 1 OW 1SOL OW 1 -0.82 15.99940 2 H 1SOLHW1 1 0.411.00800 3 H 1SOLHW2 1 0.411.00800 #endif #endif #ifdef _FF_OPLS 1 opls_116 1SOL OW 1 -0.82 2 opls_117 1SOLHW1 1 0.41 3 opls_117 1SOLHW2 1 0.41 #endif #ifdef _FF_CHARMM 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif #ifdef FLEXIBLE [ bonds ] ; ijfunctlengthforce.c. 1210.13450000.1 345000 1310.13450000.1 345000 [ angles ] ; ijkfunctangleforce.c. 2131109.47383109.47383 #else [ settles ] ; OWfunctdohdhh 110.10.16330 [ exclusions ] 123 213 312 #endif ___ 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] grompp
leila karami wrote: dear justin Fatal error: [ file spc.itp, line 46 ]: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. I checked topology file and sent topology and spc.itp file. please guide me. this is my topology file : ; Include forcefield parameters #include ffamber03.itp ; Include chain topologies #include c_A.itp #include c_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL 7127 this is my spc.itp file: Note how that in spc.itp, none of the #ifdef statements cover any of the AMBER force fields. You must either create the appropriate entry, or use a water model that is, by default, compatible with AMBER. -Justin [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifdef _FF_GROMACS 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1SOL OW 1 -0.829.95140 2 H 1SOLHW1 1 0.414.03200 3 H 1SOLHW2 1 0.414.03200 #else 1 OW 1SOL OW 1 -0.82 15.99940 2 H 1SOLHW1 1 0.411.00800 3 H 1SOLHW2 1 0.411.00800 #endif #endif #ifdef _FF_OPLS 1 opls_116 1SOL OW 1 -0.82 2 opls_117 1SOLHW1 1 0.41 3 opls_117 1SOLHW2 1 0.41 #endif #ifdef _FF_CHARMM 1 OW 1SOL OW 1 -0.82 2 HW 1SOLHW1 1 0.41 3 HW 1SOLHW2 1 0.41 #endif #ifdef FLEXIBLE [ bonds ] ; ijfunctlengthforce.c. 1210.13450000.1 345000 1310.13450000.1 345000 [ angles ] ; ijkfunctangleforce.c. 2131109.47383109.47383 #else [ settles ] ; OWfunctdohdhh 110.10.16330 [ exclusions ] 123 213 312 #endif ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] grompp
Hi, The preprocessor cuts away all parts of the [ atoms ] section in your spc.itp when you use the amber forcefield. I believe there is another version of spc.itp that comes with the amber port. Try using that one, or write your own entries in the existing file between a set of #ifdef _FF_AMBER … #endif. I recomend you do the former. /Erik leila karami skrev: dear justin Fatal error: [ file spc.itp, line 46 ]: Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. In that case move the settles section to the right molecule. I checked topology file and sent topology and spc.itp file. please guide me. this is my topology file : ; Include forcefield parameters #include ffamber03.itp ; Include chain topologies #include c_A.itp #include c_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 SOL 7127 this is my spc.itp file: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass #ifdef _FF_GROMACS 1 OW 1 SOL OW 1 -0.82 2 HW 1 SOL HW1 1 0.41 3 HW 1 SOL HW2 1 0.41 #endif #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1 SOL OW 1 -0.82 9.95140 2 H 1 SOL HW1 1 0.41 4.03200 3 H 1 SOL HW2 1 0.41 4.03200 #else 1 OW 1 SOL OW 1 -0.82 15.99940 2 H 1 SOL HW1 1 0.41 1.00800 3 H 1 SOL HW2 1 0.41 1.00800 #endif #endif #ifdef _FF_OPLS 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 1 0.41 3 opls_117 1 SOL HW2 1 0.41 #endif #ifdef _FF_CHARMM 1 OW 1 SOL OW 1 -0.82 2 HW 1 SOL HW1 1 0.41 3 HW 1 SOL HW2 1 0.41 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.47 383 109.47 383 #else [ settles ] ; OW funct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif ___ 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 -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ 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] Hello
pawan raghav wrote: I am attaching the config file which is generated on my system by using fftw-2.1.5. Please notify me where is the mistake. For future reference, ZIP archives can be inconvenient for some users (we use primarily Mac and Linux systems). There is no need to zip up a log file, just paste its text in the message. That said, there is nothing useful in the attached file. You earlier said there were problematic messages when you ran make. The output is from configuration. If you want help, you have to provide the right information. I asked about the exact error messages, taken from terminal output (or a log file, if you are saving one) that occur during compilation (the make step). There may not be anything wrong; your last message said that GROMACS compiled without a problem, so I don't fully understand what your question or concern is. -Justin -- Pawan Kumar Raghav ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] Is anyone also using lammps?s
Hi, David, I used Berendsen thermostat and a bigger tau_t=1ps to redo the simulations. The general conclusion is the same. The std err is the same in both packages. And during each simulation, the integration time does not change. Details below: Integration time step 1fs: Lammps GromacsStd.Err. (for both) Ebond(kJ/mol): 21122170 100 Eangle: 17991770 100 Etors: 25522490 100 Elj+corr: -10711 -10777 100 P(atm): 32503216 500 Integration time step 2fs: Lammps GromacsStd.Err. (for both) Ebond: 21542654 120 Eangle: 18401645 120 Etors: 25732236 120 Elj+corr: -10711 -11019 100 P(atm): 32502590 600 -Peng On Sun, 1 Nov 2009, David van der Spoel wrote: Peng Yi wrote: Thank for your reply! I have done some NVT runs per your suggestion, and the results are similar to NPT runs, i.e., Gromacs results is more affected by changing integration timestep than Lammps. Details below: A melt of 240 octane chains by united-atom model. T=300K, V=55.46 nm^3. Both Gromacs and Lammps use Nose-Hoover thermostat with tau_t=0.2 ps. As some people have note the tau_t is short for Nose Hoover. Are you sure this means the same in Lammps and in Gromacs? For one thing, there is no tau_t in the NH algorithm as far as I know, and Gromacs converts it to an appropriate weight or whatever that is called. What does Lammps do with this tau_t. To be a the safe side you could run both with Berendsen as well. Is the std err identical in both packages? And in the 2 fs run, are both simulation equlibrated with this time step as well? All other parameters in .top and .mdp files are the same as previously attached.. If I use integration time 1fs, Lammps and Gromacs produce consistent results: Lammps Gromacs std. err. Ebond(kJ/mol):21332160 100 Eangle: 17571780 80 Etors:25312510 80 Elj+corr: -10711 -10767 90 P(atm): 35003250 500 if I use integration time 2fs, Lammps results remain unchanged, but Gromacs results change significantly, particularly bonded energy: Lammps Gromacs std. err. Ebond(kJ/mol):21752710 100 Eangle: 17991640 70 Etors:25732230 80 Elj+corr: -10711 -11007 100 P(atm): 32002730 700 Would that be a result of using different integrator between Lammps and Gromacs? Lammps uses Velocity-Verlet, and Gromacs uses Leap-frog. Thanks, -Peng On Thu, 29 Oct 2009, David van der Spoel wrote: aherz wrote: Hey, are you running single or double precision gromacs? Afaik, depending on the circumstances the energy drift in gromacs can be rather bad for single precision. Please refer to the gromacs 4.0 paper for a discussion of the drift. If you want to compare energies you need the same density, which you do not have, you may need to run NVT for that. Note that your integration time step is quite large, and the temperature coupling constant is very small. You could try a shifted LJ + dispersion correction, it is not clear to me how LAMMPS treats cutoffs, couldn't find it in the manual. Alex Peng Yi schrieb: On Wed, 28 Oct 2009, Mark Abraham wrote: Peng Yi wrote: I am trying to simulate alkane melt and found out that gromacs and lammps gave different results, particularly the bonded interaction energy. I wonder if anyone has such experience. Thanks, Even two installations of the same version of GROMACS can give different results. The question is whether when using comparable model physics you observe the same ensemble averages. Mark Hi, Mark, Thanks for reply! The difference is statistically significant. And I am wondering if it is caused by the integrator: Leap-frog for Gromacs and Velocity-verlet for Lammps. Detail description of the comparison please see below: It is an NPT simulation of a melt of 240 n-octane molecules using united-atom model, i.e., CHx group is considered as one atom. There are bond, angle, torsion and LJ interactions. T=300K and P=1atm. Lammps uses nose-hoover thermostat and barostat, and Gromacs uses nose-hoover thermostat and Parranello-Rahman barostat. Time constants for thermostat and barostat are 0.02ps and 2.0ps, respectively. If I use integration time 1fs, Lammps and Gromacs gave consistent results: Lammps Gromacs Ebond(kJ/mol):2092 2146 Eangle: 1757 1760 Etors:2510 2500
[gmx-users] Re: trjcat -demux problem
Please keep all correspondence on the gmx-users list. I do not advertise myself as a private help service, and furthermore, you always stand a better chance at getting a response by posting to the list. Is this the post you're referring to? http://lists.gromacs.org/pipermail/gmx-users/2008-December/038719.html It's always best to refer directly to the thread you read. What version of Gromacs are you using? I seem to recall that the quoted error came up in 3.3.3, but not in the 4.0.x series. I never actually solved the above problem; my issue was with version 4.0.2, and it ended up being my own fault for using an improper command :) -Justin Jianhui Tian wrote: Hi Justin, I found your post on gromacs mailing list when I searched for the trjcat -demux problem. I had the same problem as you had before: Fatal error: Demuxing the same replica 4 twice at time 30.02 Unfortunately, I didn't find any successful hit to solve it on the mailing list. Could you please share with me how to solve the problem if you have solved it? Thank you very much. Jianhui -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] Is anyone also using lammps?s
Peng Yi wrote: Hi, David, I used Berendsen thermostat and a bigger tau_t=1ps to redo the simulations. The general conclusion is the same. The std err is the same in both packages. And during each simulation, the integration time does not change. Details below: Integration time step 1fs: Lammps GromacsStd.Err. (for both) Ebond(kJ/mol): 21122170 100 Eangle: 17991770 100 Etors: 25522490 100 Elj+corr: -10711 -10777 100 P(atm): 32503216 500 Integration time step 2fs: Lammps GromacsStd.Err. (for both) Ebond: 21542654 120 Eangle: 18401645 120 Etors: 25732236 120 Elj+corr: -10711 -11019 100 P(atm): 32502590 600 How about the temperature in both systems? Was Lammps also run with Berendsen? It could also still be a topology error. Maybe you can turn off the torsion potential to test this. -Peng On Sun, 1 Nov 2009, David van der Spoel wrote: Peng Yi wrote: Thank for your reply! I have done some NVT runs per your suggestion, and the results are similar to NPT runs, i.e., Gromacs results is more affected by changing integration timestep than Lammps. Details below: A melt of 240 octane chains by united-atom model. T=300K, V=55.46 nm^3. Both Gromacs and Lammps use Nose-Hoover thermostat with tau_t=0.2 ps. As some people have note the tau_t is short for Nose Hoover. Are you sure this means the same in Lammps and in Gromacs? For one thing, there is no tau_t in the NH algorithm as far as I know, and Gromacs converts it to an appropriate weight or whatever that is called. What does Lammps do with this tau_t. To be a the safe side you could run both with Berendsen as well. Is the std err identical in both packages? And in the 2 fs run, are both simulation equlibrated with this time step as well? All other parameters in .top and .mdp files are the same as previously attached.. If I use integration time 1fs, Lammps and Gromacs produce consistent results: Lammps Gromacs std. err. Ebond(kJ/mol):21332160 100 Eangle: 17571780 80 Etors:25312510 80 Elj+corr: -10711 -10767 90 P(atm): 35003250 500 if I use integration time 2fs, Lammps results remain unchanged, but Gromacs results change significantly, particularly bonded energy: Lammps Gromacs std. err. Ebond(kJ/mol):21752710 100 Eangle: 17991640 70 Etors:25732230 80 Elj+corr: -10711 -11007 100 P(atm): 32002730 700 Would that be a result of using different integrator between Lammps and Gromacs? Lammps uses Velocity-Verlet, and Gromacs uses Leap-frog. Thanks, -Peng On Thu, 29 Oct 2009, David van der Spoel wrote: aherz wrote: Hey, are you running single or double precision gromacs? Afaik, depending on the circumstances the energy drift in gromacs can be rather bad for single precision. Please refer to the gromacs 4.0 paper for a discussion of the drift. If you want to compare energies you need the same density, which you do not have, you may need to run NVT for that. Note that your integration time step is quite large, and the temperature coupling constant is very small. You could try a shifted LJ + dispersion correction, it is not clear to me how LAMMPS treats cutoffs, couldn't find it in the manual. Alex Peng Yi schrieb: On Wed, 28 Oct 2009, Mark Abraham wrote: Peng Yi wrote: I am trying to simulate alkane melt and found out that gromacs and lammps gave different results, particularly the bonded interaction energy. I wonder if anyone has such experience. Thanks, Even two installations of the same version of GROMACS can give different results. The question is whether when using comparable model physics you observe the same ensemble averages. Mark Hi, Mark, Thanks for reply! The difference is statistically significant. And I am wondering if it is caused by the integrator: Leap-frog for Gromacs and Velocity-verlet for Lammps. Detail description of the comparison please see below: It is an NPT simulation of a melt of 240 n-octane molecules using united-atom model, i.e., CHx group is considered as one atom. There are bond, angle, torsion and LJ interactions. T=300K and P=1atm. Lammps uses nose-hoover thermostat and barostat, and Gromacs uses nose-hoover thermostat and Parranello-Rahman barostat. Time constants for thermostat and barostat are 0.02ps and 2.0ps, respectively. If I use integration time 1fs, Lammps and
Re: [gmx-users] try to restart a md run using cpt file
Thielges, Sabine wrote: Reading file md_20_100_s_IP_beta.tpr, VERSION 4.0.3 (single precision) Reading checkpoint file md_20_100_s_IP_beta_prev.cpt generated: Sat Oct 31 12:34:46 2009 --- Program mdrun.MPI, VERSION 4.0.3 Source code file: checkpoint.c, line: 1238 Fatal error: Truncation of file md_20_100_s_IP_beta.trr failed. --- This issue has come up before. You can check the integrity of the .trr file with gmxcheck; there may be an incomplete frame. You might also consider upgrading to the latest version (4.0.5) and try again, otherwise if this is a bug (I can't remember), it would only be fixed in the development code in the git repository. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] Re: trjcat -demux problem
I solved the problem. The command that works is: trjcat -f md00.xtc md01.xtc ... md0N.xtc -o out00.xtc out01.xtc ... out0N.xtc -s replica_index.xvg Jianhui Date: Tue, 03 Nov 2009 10:24:12 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: [gmx-users] Re: trjcat -demux problem To: Jianhui Tian ti...@rpi.edu, Gromacs Users' List gmx-users@gromacs.org Message-ID: 4af04b1c.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Please keep all correspondence on the gmx-users list. I do not advertise myself as a private help service, and furthermore, you always stand a better chance at getting a response by posting to the list. Is this the post you're referring to? http://lists.gromacs.org/pipermail/gmx-users/2008-December/038719.html It's always best to refer directly to the thread you read. What version of Gromacs are you using? I seem to recall that the quoted error came up in 3.3.3, but not in the 4.0.x series. I never actually solved the above problem; my issue was with version 4.0.2, and it ended up being my own fault for using an improper command :) -Justin Jianhui Tian wrote: Hi Justin, I found your post on gromacs mailing list when I searched for the trjcat -demux problem. I had the same problem as you had before: Fatal error: Demuxing the same replica 4 twice at time 30.02 Unfortunately, I didn't find any successful hit to solve it on the mailing list. Could you please share with me how to solve the problem if you have solved it? Thank you very much. Jianhui ___ 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] try to restart a md run using cpt file
Paymon Pirzadeh wrote: Hello, To restart a run for continuation, which .cpt file should be used? the one with the outputname.cpt or the outputname_prev.cpt? The most recent. The _prev name indicates that it is a backup in case the newest one fails or has a problem. Run gmxcheck on each of them to see for yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] Is anyone also using lammps?s
I turned off the torsion interaction. The difference between Lammps and Gromacs at integration time step 2fs was reduced. Details below: A melt of 240 n-octane (united-atom model), NVT, T=300K, V=55.46nm^3. Both Lammps and Gromacs use berendsen thermostat with tau_t=1ps. Integration time step 1fs: LammpsGromacsStd. Err. (for both) Ebond(kJ/mol):2092 2109 100 Eangle: 1778 175480 Elj+corr: -10501-10553 100 T(K): 300 299 5 P(atm): 3188 3016 700 integration time step 2fs: LammpsGromacsStd.Err. (for both) Ebond:2133 2232 100 Eangle: 1803 173780 Elj+corr: -10501-10623 100 T: 300 298 5 P:3133 2955 600 Lammps results remain almost unchanged when dt increases from 1fs to 2fs, and Ebond : Eangle = 7 : 6, which is the ratio between # of bonds and # of angles. Gromacs results change more significantly when dt goes from 1fs to 2fs. and the trend of Ebond and Eangle are opposite. It is more significant when torsion interaction is present. On Tue, 3 Nov 2009, David van der Spoel wrote: Peng Yi wrote: Hi, David, I used Berendsen thermostat and a bigger tau_t=1ps to redo the simulations. The general conclusion is the same. The std err is the same in both packages. And during each simulation, the integration time does not change. Details below: Integration time step 1fs: Lammps GromacsStd.Err. (for both) Ebond(kJ/mol): 21122170 100 Eangle: 17991770 100 Etors: 25522490 100 Elj+corr: -10711 -10777 100 P(atm): 32503216 500 Integration time step 2fs: Lammps GromacsStd.Err. (for both) Ebond: 21542654 120 Eangle: 18401645 120 Etors: 25732236 120 Elj+corr: -10711 -11019 100 P(atm): 3250 2590 600 How about the temperature in both systems? Was Lammps also run with Berendsen? It could also still be a topology error. Maybe you can turn off the torsion potential to test this. -Peng On Sun, 1 Nov 2009, David van der Spoel wrote: Peng Yi wrote: Thank for your reply! I have done some NVT runs per your suggestion, and the results are similar to NPT runs, i.e., Gromacs results is more affected by changing integration timestep than Lammps. Details below: A melt of 240 octane chains by united-atom model. T=300K, V=55.46 nm^3. Both Gromacs and Lammps use Nose-Hoover thermostat with tau_t=0.2 ps. As some people have note the tau_t is short for Nose Hoover. Are you sure this means the same in Lammps and in Gromacs? For one thing, there is no tau_t in the NH algorithm as far as I know, and Gromacs converts it to an appropriate weight or whatever that is called. What does Lammps do with this tau_t. To be a the safe side you could run both with Berendsen as well. Is the std err identical in both packages? And in the 2 fs run, are both simulation equlibrated with this time step as well? All other parameters in .top and .mdp files are the same as previously attached.. If I use integration time 1fs, Lammps and Gromacs produce consistent results: Lammps Gromacs std. err. Ebond(kJ/mol):21332160 100 Eangle: 17571780 80 Etors:25312510 80 Elj+corr: -10711 -10767 90 P(atm): 35003250 500 if I use integration time 2fs, Lammps results remain unchanged, but Gromacs results change significantly, particularly bonded energy: Lammps Gromacs std. err. Ebond(kJ/mol):21752710 100 Eangle: 17991640 70 Etors:25732230 80 Elj+corr: -10711 -11007 100 P(atm): 3200 2730 700 Would that be a result of using different integrator between Lammps and Gromacs? Lammps uses Velocity-Verlet, and Gromacs uses Leap-frog. Thanks, -Peng On Thu, 29 Oct 2009, David van der Spoel wrote: aherz wrote: Hey, are you running single or double precision gromacs? Afaik, depending on the circumstances the energy drift in gromacs can be rather bad for single precision. Please refer to the gromacs 4.0 paper for a discussion of the drift. If you want to compare energies you need the same density, which you do not have, you may need to run NVT for that. Note that your integration time step is quite large, and the temperature coupling constant is very small. You could try a shifted LJ + dispersion
[gmx-users] g_angle between center of mass of three groups
Hi, I know that g_dist gives the distance between the center of masses of two groups. But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three groups. If not, In that case, can anyone suggest suggest any other alternative ? Jagannath Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew___ 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] try to restart a md run using cpt file
Hello, To restart a run for continuation, which .cpt file should be used? the one with the outputname.cpt or the outputname_prev.cpt? Payman ___ 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] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms
Chandan Choudhury wrote: Hi everyone !! I am having a problem using pdb2gmx command. Using the command on my input pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms. I do not have only O either in input pdb file or in rtp file. and its O and not 0 (zero). My part of input files reads as ATOM 1 NCCMT 1 -2.521 -2.813 2.083 0.00 0.00 ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00 ATOM 3 CCCMT 1 -1.711 -0.842 0.859 0.00 0.00 ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00 ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00 ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00 ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00 ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00 ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00 ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00 ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00 ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00 ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00 ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00 ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00 ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00 ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00 ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00 ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00 ATOM 20 HCCMT 1 -1.801 -3.362 1.658 0.00 0.00 ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00 ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00 ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00 ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00 ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00 ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00 ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00 ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00 ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00 ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00 ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00 ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00 ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00 ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00 ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00 ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00 ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00 ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00 What's next in the input PDB file? Mark and my part of .rtp file is [ CCMT ] [ atoms ] Namber99_34 -0.3961651 Hamber99_17 0.2951872 CAamber99_11 -0.0735013 HAamber99_19 0.1405104 CBamber99_11 -0.2213715 HB1amber99_19 0.1465376 HB2amber99_19 0.1465377 SGamber99_48 -0.2851828 SDamber99_68 -0.089 ;SM CEamber99_69 -0.10 10 HE1amber99_70 -0.09 11 HE2amber99_70 -0.09 12 CZamber99_71 -0.003 13 CHamber99_73 0.334 14 CH1amber99_74 -0.337 15 HH11amber99_76 0.090 16 HH12amber99_76 0.090 17 HH13amber99_76 0.090 18 CH2amber99_74 -0.337 19 HH21amber99_76 0.090 20 HH22amber99_76 0.090 21 HH23amber99_76 0.090 22 NT1amber99_77 0.220 23 OT1amber99_78 -0.438 24 CIamber99_75 0.329 25 CI1amber99_74 -0.337 26 HI11amber99_76 0.090 27 HI12amber99_76 0.090 28 HI13amber99_76 0.090 29 CI2amber99_74 -0.337 30 HI21amber99_76 0.090 31 HI22amber99_76 0.090 32 HI23amber99_76 0.090 33 CKamber99_72 -0.340 34 HKamber99_79 0.162 35 Camber99_20.643035 36 OC1amber99_45 -0.7981037 OC2amber99_45 -0.7981038 Any help is heartly welcomed. Thanks in advance Chandan -- Chandan kumar Choudhury NCL, Pune INDIA ___ 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] g_angle between center of mass of three groups
jagannath mondal wrote: Hi, I know that g_dist gives the distance between the center of masses of two groups. But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three groups.If not, In that case, can anyone suggest suggest any other alternative ? You should start by reading g_angle -h and g_sgangle -h. g_angle will calculate the average over a group of angles, which is similar to what you want. 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] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms
Chandan Choudhury wrote: My complete input file is ATOM 1 NCCMT 1 -2.521 -2.813 2.083 0.00 0.00 ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00 ATOM 3 CCCMT 1 -1.711 -0.842 0.859 0.00 0.00 ATOM 4 CB CCMT 1 -4.034 -0.895 1.821 0.00 0.00 ATOM 5 SG CCMT 1 -4.523 0.408 0.710 0.00 0.00 ATOM 6 SD CCMT 1 -5.981 1.512 1.567 0.00 0.00 ATOM 7 CE CCMT 1 -7.394 0.480 1.895 0.00 0.00 ATOM 8 CZ CCMT 1 -6.988 -0.662 2.846 0.00 0.00 ATOM 9 CH CCMT 1 -7.604 -2.072 2.895 0.00 0.00 ATOM 10 CH1 CCMT 1 -8.797 -2.090 3.869 0.00 0.00 ATOM 11 CH2 CCMT 1 -8.096 -2.574 1.525 0.00 0.00 ATOM 12 CI CCMT 1 -5.986 -1.995 4.476 0.00 0.00 ATOM 13 CI1 CCMT 1 -4.582 -2.406 4.958 0.00 0.00 ATOM 14 CI2 CCMT 1 -6.931 -2.001 5.692 0.00 0.00 ATOM 15 CK CCMT 1 -6.018 -0.615 3.792 0.00 0.00 ATOM 16 NT1 CCMT 1 -6.486 -2.876 3.411 0.00 0.00 ATOM 17 OC1 CCMT 1 -0.511 -1.346 0.867 0.00 0.00 ATOM 18 OC2 CCMT 1 -1.885 0.420 0.592 0.00 0.00 ATOM 19 OT1 CCMT 1 -6.836 -4.122 3.830 0.00 0.00 ATOM 20 HCCMT 1 -1.801 -3.362 1.658 0.00 0.00 ATOM 21 HA CCMT 1 -3.292 -2.165 0.256 0.00 0.00 ATOM 22 HB1 CCMT 1 -4.878 -1.518 2.033 0.00 0.00 ATOM 23 HB2 CCMT 1 -3.668 -0.468 2.731 0.00 0.00 ATOM 24 HE1 CCMT 1 -7.754 0.067 0.976 0.00 0.00 ATOM 25 HE2 CCMT 1 -8.165 1.065 2.350 0.00 0.00 ATOM 26 HH11 CCMT 1 -9.175 -3.088 3.952 0.00 0.00 ATOM 27 HH21 CCMT 1 -8.875 -1.932 1.170 0.00 0.00 ATOM 28 HH12 CCMT 1 -8.477 -1.749 4.832 0.00 0.00 ATOM 29 HH22 CCMT 1 -7.283 -2.566 0.829 0.00 0.00 ATOM 30 HH13 CCMT 1 -9.567 -1.446 3.500 0.00 0.00 ATOM 31 HH23 CCMT 1 -8.471 -3.571 1.624 0.00 0.00 ATOM 32 HI11 CCMT 1 -4.241 -1.712 5.697 0.00 0.00 ATOM 33 HI21 CCMT 1 -6.956 -2.982 6.119 0.00 0.00 ATOM 34 HI12 CCMT 1 -4.624 -3.387 5.383 0.00 0.00 ATOM 35 HI22 CCMT 1 -6.577 -1.303 6.422 0.00 0.00 ATOM 36 HI13 CCMT 1 -3.906 -2.405 4.128 0.00 0.00 ATOM 37 HI23 CCMT 1 -7.915 -1.722 5.380 0.00 0.00 ATOM 38 HK CCMT 1 -5.391 0.221 4.019 0.00 0.00 ATOM 39 NNARG 2 -4.657 -5.920 2.257 0.00 0.00 ATOM 40 CA NARG 2 -3.476 -5.161 2.694 0.00 0.00 ATOM 41 CNARG 2 -3.680 -3.668 2.378 0.00 0.00 ATOM 42 ONARG 2 -4.839 -3.179 2.371 0.00 0.00 ATOM 43 CB NARG 2 -2.230 -5.679 1.952 0.00 0.00 ATOM 44 CG NARG 2 -0.992 -4.885 2.410 0.00 0.00 ATOM 45 CZ NARG 2 2.459 -4.459 1.265 0.00 0.00 ATOM 46 CD NARG 2 0.254 -5.404 1.668 0.00 0.00 ATOM 47 NE NARG 2 1.436 -4.648 2.106 0.00 0.00 ATOM 48 NH1 NARG 2 2.406 -4.958 0.025 0.00 0.00 ATOM 49 NH2 NARG 2 3.535 -3.771 1.664 0.00 0.00 ATOM 50 HA NARG 2 -3.341 -5.287 3.748 0.00 0.00 ATOM 51 HB1 NARG 2 -2.089 -6.716 2.172 0.00 0.00 ATOM 52 HB2 NARG 2 -2.365 -5.552 0.898 0.00 0.00 ATOM 53 HG1 NARG 2 -1.132 -3.847 2.190 0.00 0.00 ATOM 54 HG2 NARG 2 -0.858 -5.011 3.464 0.00 0.00 ATOM 55 HD1 NARG 2 0.393 -6.442 1.888 0.00 0.00 ATOM 56 HD2 NARG 2 0.120 -5.278 0.614 0.00 0.00 ATOM 57 HE NARG 2 1.475 -4.274 3.033 0.00 0.00 ATOM 58 HH11 NARG 2 1.602 -5.472 -0.274 0.00 0.00 ATOM 59 HH21 NARG 2 3.574 -3.398 2.591 0.00 0.00 ATOM 60 HH12 NARG 2 3.171 -4.817 -0.604 0.00 0.00 ATOM 61 HH22 NARG 2 4.299 -3.631 1.035 0.00 0.00 ATOM 62 H1 NARG 2 -5.466 -5.584 2.740 0.00 0.00 ATOM 63 H2 NARG 2 -4.525 -6.890 2.463 0.00 0.00 ATOM 64 H3 NARG 2 -4.783 -5.802 1.272 0.00 0.00 END This looks like you are trying to convert a non-covalently-bound ligand and an ARG-terminated protein in the same structure. If you'd described what you were trying to do in words in your first post, that would have been helpful. Your approach might work if you use PDB chain identifiers properly. Also possible is to run pdb2gmx on isolated ligand, and separately on isolated protein. Edit the two top files to convert them to .itp files, and #include them in a new master .top file. This might be a good idea for some workflows. See http://www.gromacs.org/Documentation/File_Formats/.top_File and links from it. Mark On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham mark.abra...@anu.edu.au
