[gmx-users] problem regarding pbc
Dear GROMACS list members, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that FATAL error, CL atom type can not be found,I can not understand the problem. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ 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] problem regarding pbc
Hi Sangeeta, To start with, you don't really describe a problem regarding pbc, as you've stated in the subject. Please make the subject reflect your problem or question directly. This will make it easier on the repliers on this list to check whether they can be of any help. Most of us read/discard messages based on the subject. Now, you have three questions, which you've stated before, but apparently the answers were not informative enough. To start with the pbc, gromacs uses pbc unless explicitly stated otherwise, by adding pbc=no in the .mdp file. Regarding the chlorides, I think you caught that you have to have an #include statement in the .top file, reading #include ions.itp. The next thing to make sure is that the name you've used for your chloride ions in the .top file matches those in the file ions.itp listed for the force field you are using. It may be CL, Cl, Cl-. You can try either or you can check the file ions.itp in your $GMXDIR/share/gromacs/top directory. Finally, regarding dssp, please explain what you tried to do, i.e. which command you've issued. Note that the file you mentioned is merely a temporary file. Hope it helps, Tsjerk On 1/24/07, sangeeta [EMAIL PROTECTED] wrote: Dear GROMACS list members, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that FATAL error, CL atom type can not be found,I can not understand the problem. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] problem regarding dssp
dear Sir, Thanks a lot for your reply.I am sorry for the fact that my subject name does not tally with the problem I faced.I really apologize for that. So I do not need to include explicitely pbc=xyz in my .mdp file as it is already being used by default. Regarding dssp I used the following commands export DSSP=/home/debjani/dssp setenv DSSP /home/debjani/dssp do_dssp -s md.tpr -f traj.xtc At the end of the program only the files namely ddEZ117f ddOWnvlx etc were present, but no .xpm files were there.I want to get the plot of changing of secondary structural elements during the run.PLease help. regards Sangeeta On Wed, 24 Jan 2007 09:45:02 +0100, Tsjerk Wassenaar wrote Hi Sangeeta, To start with, you don't really describe a problem regarding pbc, as you've stated in the subject. Please make the subject reflect your problem or question directly. This will make it easier on the repliers on this list to check whether they can be of any help. Most of us read/discard messages based on the subject. Now, you have three questions, which you've stated before, but apparently the answers were not informative enough. To start with the pbc, gromacs uses pbc unless explicitly stated otherwise, by adding pbc=no in the .mdp file. Regarding the chlorides, I think you caught that you have to have an #include statement in the .top file, reading #include ions.itp. The next thing to make sure is that the name you've used for your chloride ions in the .top file matches those in the file ions.itp listed for the force field you are using. It may be CL, Cl, Cl-. You can try either or you can check the file ions.itp in your $GMXDIR/share/gromacs/top directory. Finally, regarding dssp, please explain what you tried to do, i.e. which command you've issued. Note that the file you mentioned is merely a temporary file. Hope it helps, Tsjerk On 1/24/07, sangeeta [EMAIL PROTECTED] wrote: Dear GROMACS list members, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that FATAL error, CL atom type can not be found,I can not understand the problem. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 -- Open WebMail Project (http://openwebmail.org) ___ 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] problem regarding dssp
dear Sir, Thanks a lot for your reply.I am sorry for the fact that my subject name does not tally with the problem I faced.I really apologize for that. So I do not need to include explicitely pbc=xyz in my .mdp file as it is already being used by default. Regarding dssp I used the following commands export DSSP=/home/debjani/dssp setenv DSSP /home/debjani/dssp do_dssp -s md.tpr -f traj.xtc At the end of the program only the files namely ddEZ117f ddOWnvlx etc were present, but no .xpm files were there.I want to get the plot of changing of secondary structural elements during the run.PLease help. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ 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] problem regarding dssp
dear Sir, Thanks a lot for your reply.I am sorry for the fact that my subject name does not tally with the problem I faced.I really apologize for that. So I do not need to include explicitely pbc=xyz in my .mdp file as it is already being used by default. Regarding dssp I used the following commands export DSSP=/home/debjani/dssp setenv DSSP /home/debjani/dssp do_dssp -s md.tpr -f traj.xtc At the end of the program only the files namely ddEZ117f ddOWnvlx etc were present, but no .xpm files were there.I want to get the plot of changing of secondary structural elements during the run.PLease help. regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ 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] problem regarding dssp
Hi Sangeeta, export DSSP=/home/debjani/dssp This is needed if your shell is bash setenv DSSP /home/debjani/dssp This is needed if your shell is (t)csh Now, /home/debjani/dssp points to the file dssp and not to the directory, right? do_dssp -s md.tpr -f traj.xtc Could you send the output of the command? That is likely to be more informative. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] generation of a box of water
Hi, I am trying to generate a box of purely water molecules (101 molecules) using the following commands: /usr/local/gromacs/bin/genbox -cp box.pdb -ci spc216 -o water.pdb -nmol 101 (I've also tried using tip5p but have the same problem.) box.pdb looks like this: TITLE NOTHING REMARKTHIS IS A SIMULATION BOX CRYST19.7404 14.9488 20.0870 90.00 90.00 90.00 P 1 1 MODEL1 TER ENDMDL The box that is generated has too many close contacts... Even after energy minimization, there are atoms too close together. I've played around with -seed, varying between 20 and 2050 but whatever value I use, the system will not minimise to a sensible enough configuration (ie: forces 1003 or more). The .mdp file looks like this: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = l-bfgs ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 100 rlist= 0.4 rcoulomb = 0.4 rvdw = 0.4 ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1 emstep = 0.1 nstcgsteep = 1000 I've used steep and l-bfgs, the latter of which seems to be slightly more effective but even so if I try to run an MD on the system from the configuration I get this error: Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 280 ] Please report this to the mailing list (gmx-users@gromacs.org) NB: We are using V 3.3.1 of gromacs. Please help! Kat ___ 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] Quantical Atoms
Please, How can I compile the GROMACS QM/MM (with MOPAC) and with more than 161 quantical atoms? I have change the SIZE file of MOPAC package but my jobs only run with less then 161 quantical atoms. Very thanks, Arlan da Silva Gonçalves ___ 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] Info on g_sas DGsolv
Dear All I have one question regarding the output of g_sas. In the area.xvg file that includes the hydrophobic,hydrophilic and total solvent accessible surface, also includeas a DGsolv output. I tried to find what is kind of energy (is it the total solvatation energy?) and what are the units (I am assuming kJ/mol) but I did not found it. Could somebody ellucidate me? Thanks! Cheers Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ 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] pdbgmx warning long bond
Dear Gromacs Users, I am trying to simulate a peptide in explicit lipid bilayer membrane environment (say, DPCC). I took well equilibrated dppc.pdb file from Dr. Peter tieleman site and i modified it put in the names of the atoms of the ffG53a5.rtp file . I changed DPPC x DPP in ffG53a5.rtp file. But when executing pdb2gmx ( pdb2gmx_331 -f input.pdb -o output.gro -p output.top -i output.itp -ffG53a5 -water spc -ignh) i 've gived some errors. The long bonds are in the atoms of the membrane. Why it could be? Could anybody give me a pointer to a more elaborated protocol in setting up and running this type of simulation using gromacs? This is my first simulation. This is my output.pdb2gmx_331 file: Opening library file ffG53a5.rtp Opening library file aminoacids.dat Opening library file /usr/local/gromacs331/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully All occupancies are one Opening library file ffG53a5.atp Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Opening library file ffG53a5.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Sorting it all out... Opening library file ffG53a5.hdb Opening library file /usr/local/gromacs331/share/gromacs/top/ffG53a5-n.tdb Opening library file /usr/local/gromacs331/share/gromacs/top/ffG53a5-c.tdb There are 41 donors and 42 acceptors There are 55 hydrogen bonds Opening library file /usr/local/gromacs331/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Making bonds... Opening library file aminoacids.dat Number of bonds was 282, now 277 Generating angles, dihedrals and pairs... Before cleaning: 477 pairs Before cleaning: 501 dihedrals There are 150 dihedrals, 119 impropers, 402 angles 477 pairs, 277 bonds and 0 virtual sites Total mass 3129.726 a.m.u. Total charge 1.000 e Writing topology There are 64 donors and 0 acceptors There are 0 hydrogen bonds Opening library file /usr/local/gromacs331/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully Making bonds... Warning: Long Bond (155-156 = 4.66174 nm) Warning: Long Bond (161-162 = 4.76126 nm) Warning: Long Bond (198-199 = 4.66509 nm) Warning: Long Bond (436-437 = 4.20115 nm) Warning: Long Bond (438-439 = 4.13177 nm) Warning: Long Bond (439-440 = 4.17203 nm) Warning: Long Bond (440-441 = 4.14281 nm) Warning: Long Bond (796-797 = 4.6577 nm) Warning: Long Bond (855-856 = 4.62827 nm) Warning: Long Bond (876-877 = 4.71688 nm) Warning: Long Bond (993-994 = 4.09589 nm) Warning: Long Bond (1070-1071 = 4.11 nm) Warning: Long Bond (1094-1095 = 4.10309 nm) Warning: Long Bond (1113-1132 = 4.15103 nm) Warning: Long Bond (1134-1136 = 4.59357 nm) Warning: Long Bond (1141-1142 = 4.59602 nm) Warning: Long Bond (1163-1182 = 4.59533 nm) Warning: Long Bond (1171-1172 = 4.57689 nm) Warning: Long Bond (1224-1225 = 4.68619 nm) Warning: Long Bond (1230-1231 = 4.59582 nm) Warning: Long Bond (1384-1386 = 4.17214 nm) Warning: Long Bond (1386-1387 = 4.13444 nm) Warning: Long
Re: [gmx-users] Info on g_sas DGsolv
Afonso Duarte wrote: Dear All I have one question regarding the output of g_sas. In the area.xvg file that includes the hydrophobic,hydrophilic and total solvent accessible surface, also includeas a DGsolv output. I tried to find what is kind of energy (is it the total solvatation energy?) and what are the units (I am assuming kJ/mol) but I did not found it. Could somebody ellucidate me? Thanks! Cheers Afonso DGsolv in kJ/mol, according to Eisenberg (the ref is printed) -- 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] How to implement dihedral restraints
Hi, The test I ran was just rotating a side chain of an amino acid residue over one of its dihedral angle 360 degrees with dihre_fc = 8000. OK. I was doing a val sidechain. I originally thought fc = 8000kJ/mol unit^2 would give fluctuation of about the half the unit size since I use fc = 8000kJ/mol nm^2 for 0.5A spacing. But, after I thought twice about it, it would be fc = 80kJ/moml nm^2, for 0.5nm spacing... So, after I realized that, kJ/mol rad^2 made sense to me and my test run's fluctuation (about several degress = 1/20 rad = about 3 degrees) OK. I was doing my valine sidechain with about 26 umbrellas using force constants ranging from around 100 kJ/mol*rad^2 to 500 kJ/mol*rad^2 (bigger force constants when the PMF is steep). I wish I had an adaptive scheme for picking force constants, but I just did this by trial and error to get good overlap with as small a number of umbrellas as possible. I guess the other way is what it sounds like you're talking about doing -- just put umbrellas with tight springs every couple degrees. It is probably important to make a plot of your binned dihedral angles at the end to make sure you have sufficient overlap. David ___ 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] MD Error after adding a unnatural amio acid
Hi Everyone, I once talked about this before and have new problem now. The new group was successfully attached to the protein, but problem comes during the process of MD. The error messages are always like the following with either new linkage broken or a neighboring Hydrogen flying away. Parameters except for partial charge are perfectly okay. The partial charges from HF calculations even made it worse, because of different scheme with gmx. I also tried to partition the new bulky group into small fragments when T-coupling, but did not help. I am wondering what the reasons are. Is the new group too big? What is the alternative to assign partial charge in gmx other than PRODRG? Wishes, Liu, Yuemin Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 4.40414e+037.17452e+033.03251e+03 2.44614e+032.21377e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 4.01788e+042.57243e+05 -1.94251e+06 -2.87497e+05 -1.91331e+06 Kinetic En. Total EnergyTemperature Pressure (bar) 3.45332e+05 -1.56798e+062.99118e+02 -1.03238e+01 Shake did not converge in 1000 steps i mi j mj before after should be 3173 14.01 3174 1.01 0.1 0.15192 0.1 Constraint error in algorithm Shake at step 650187 Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ 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] generation of a box of water
I think you are getting that error about NaN because you have water molecules that are almost exactly on top of one another. If you just want a box of water, the easiest way to do it is this: genbox -cs -o water.pdb -box x y z Here, x y and z are the box dimensions in nanometers. You can play with the box dimensions to get close to the desired number of waters. Bob On 24 Jan 2007 08:19:36 +, K.F. Austen [EMAIL PROTECTED] wrote: Hi, I am trying to generate a box of purely water molecules (101 molecules) using the following commands: /usr/local/gromacs/bin/genbox -cp box.pdb -ci spc216 -o water.pdb -nmol 101 (I've also tried using tip5p but have the same problem.) box.pdb looks like this: TITLE NOTHING REMARKTHIS IS A SIMULATION BOX CRYST19.7404 14.9488 20.0870 90.00 90.00 90.00 P 1 1 MODEL1 TER ENDMDL The box that is generated has too many close contacts... Even after energy minimization, there are atoms too close together. I've played around with -seed, varying between 20 and 2050 but whatever value I use, the system will not minimise to a sensible enough configuration (ie: forces 1003 or more). The .mdp file looks like this: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = l-bfgs ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 100 rlist= 0.4 rcoulomb = 0.4 rvdw = 0.4 ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1 emstep = 0.1 nstcgsteep = 1000 I've used steep and l-bfgs, the latter of which seems to be slightly more effective but even so if I try to run an MD on the system from the configuration I get this error: Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 280 ] Please report this to the mailing list (gmx-users@gromacs.org) NB: We are using V 3.3.1 of gromacs. Please help! Kat ___ 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 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] problem regarding pbc
Tsjerk, Your problem is met also when we tried to install gromacs3.3. The administrator pf the HPC cluster tries to find a solution. If not, I will fix a meeting with him. Between I might try myself some other variants. best regards Nicu On Wed, 24 Jan 2007 09:45:02 +0100 Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Sangeeta, To start with, you don't really describe a problem regarding pbc, as you've stated in the subject. Please make the subject reflect your problem or question directly. This will make it easier on the repliers on this list to check whether they can be of any help. Most of us read/discard messages based on the subject. Now, you have three questions, which you've stated before, but apparently the answers were not informative enough. To start with the pbc, gromacs uses pbc unless explicitly stated otherwise, by adding pbc=no in the .mdp file. Regarding the chlorides, I think you caught that you have to have an #include statement in the .top file, reading #include ions.itp. The next thing to make sure is that the name you've used for your chloride ions in the .top file matches those in the file ions.itp listed for the force field you are using. It may be CL, Cl, Cl-. You can try either or you can check the file ions.itp in your $GMXDIR/share/gromacs/top directory. Finally, regarding dssp, please explain what you tried to do, i.e. which command you've issued. Note that the file you mentioned is merely a temporary file. Hope it helps, Tsjerk On 1/24/07, sangeeta [EMAIL PROTECTED] wrote: Dear GROMACS list members, I have three questions, My protein has +2 charge, so I added two Cl atoms through the program genion and subsequently edited the topol.top file, in spite of that while running mdrun it gave an error that FATAL error, CL atom type can not be found,I can not understand the problem. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? Waiting for your reply. regards SANGEETA -- Open WebMail Project (http://openwebmail.org) ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 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] compile Gromacs 3.2.1: line 0: unexpected EOF while looking for matching `'
I'm trying to compile Gromacs 3.2.1 (a user requested this version specifically). The configure succeeds, however make fails with: /bin/sh: -c: line 0: unexpected EOF while looking for matching `' /bin/sh: -c: line 1: syntax error: unexpected end of file The system is a 64bit RHEL 4 workstation, I'm using Intel Compilers: v 9.1.042 Any idea what the heck it's complaining about? Here's my configure statement: ./configure CC=icc CXX=icpc FC=ifort F77=ifort F90=ifort --enable-sse --enable-fortran --prefix=/share/apps/gromacs/intel/gromacs-3.2.1-s64 Here's the last several lines of the make output: if /bin/sh ../../libtool --mode=compile icc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\/share/apps/gromac s/intel/gromacs-3.2.1-s64/share/top\ -I/share/apps/intel/cce/9.1.042/include -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/ usr/include/libxml2 -O3 -I/usr/include/libxml2 -MT widget.lo -MD -MP -MF .deps/widget.Tpo \ -c -o widget.lo `test -f 'widget.c' || echo './'`widget.c; \ then mv -f .deps/widget.Tpo .deps/widget.Plo; \ else rm -f .deps/widget.Tpo; exit 1; \ fi icc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\/share/apps/gromacs/intel/gromacs-3.2.1-s64/share/top\ -I/ share/apps/intel/cce/9.1.042/include -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/usr/include/libxml2 -O3 -I/usr/include/li bxml2 -MT widget.lo -MD -MP -MF .deps/widget.Tpo -c widget.c -o widget.o /bin/sh ../../libtool --mode=link icc -O3 -I/usr/include/libxml2 -L/share/apps/intel/cce/9.1.042/lib -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/ usr/X11R6/lib -o libgmx.la -rpath /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib -version-info 3:0:0 3dview.lo atomprop.loblock_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gb util.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo nam es.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo s hift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgm s.lo wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo mgmx.lo widget.lo -L/usr/ X11R6/lib64 -lnsl -lsrfftw -lsfftw -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -lxml2 -lz -lpthread -lm -L/share/apps/intel/cce/9.1.042/lib -L/share/ap ps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib -L/usr/X11R6/lib -L/share/apps/intel/fce/9.1.036/lib -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -L/u sr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -lsvml -lifport -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl /bin/sh: -c: line 0: unexpected EOF while looking for matching `' /bin/sh: -c: line 1: syntax error: unexpected end of file make[3]: *** [libgmx.la] Error 2 make[3]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' make: *** [all-recursive] Error 1 Making install in src make[1]: Entering directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src' Making install in gmxlib make[2]: Entering directory `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib' /bin/sh ../../libtool --mode=link icc -O3 -I/usr/include/libxml2 -L/share/apps/intel/cce/9.1.042/lib -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/ usr/X11R6/lib -o libgmx.la -rpath /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib -version-info 3:0:0 3dview.lo atomprop.loblock_tx.lo bondfree.lo calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gb util.lo fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo mvxvf.lo nam es.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo readinp.lo replace.lo rmpbc.lo s hift_util.lo sortwater.lo smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgm s.lo wman.lo writeps.lo xdrd.lo
Re: [gmx-users] MD Error after adding a unnatural amio acid
Hi Liu yuemin, Now I haven't got a clue of what you're trying to do! Okay, add a new group somewhere and do MD... First of all, what is the group you're talking about? How did you link it. You mention the linkage being broken, but you're not doing QM; bonds stay bonds, but may go well out of bounds. Did you perform energy minimization? Did you check the stability of the group alone in solution? You talk about different groups for temperature coupling? Maybe give the tc_coupl related lines from the .mdp files? Note that you shouldn't couple such a group separately. Or do you mean charge groups? Please try to be clear on such things. Anyway, at this point the partial charges seem to be the least of your worries (unless you have a collection of -1,+1 or worse stuck together). I suspect your trouble is related to the building block. Cheers, Tsjerk On 1/24/07, yuemin liu [EMAIL PROTECTED] wrote: Hi Everyone, I once talked about this before and have new problem now. The new group was successfully attached to the protein, but problem comes during the process of MD. The error messages are always like the following with either new linkage broken or a neighboring Hydrogen flying away. Parameters except for partial charge are perfectly okay. The partial charges from HF calculations even made it worse, because of different scheme with gmx. I also tried to partition the new bulky group into small fragments when T-coupling, but did not help. I am wondering what the reasons are. Is the new group too big? What is the alternative to assign partial charge in gmx other than PRODRG? Wishes, Liu, Yuemin Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 4.40414e+037.17452e+033.03251e+03 2.44614e+032.21377e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 4.01788e+042.57243e+05 -1.94251e+06 -2.87497e+05 -1.91331e+06 Kinetic En. Total EnergyTemperature Pressure (bar) 3.45332e+05 -1.56798e+062.99118e+02 -1.03238e+01 Shake did not converge in 1000 steps i mi j mj before after should be 3173 14.01 3174 1.01 0.1 0.15192 0.1 Constraint error in algorithm Shake at step 650187 Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] pdbgmx warning long bond
Hi Maite, pdb2gmx tries to tie your lipids together. Don't run the membrane through pdb2gmx. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] LINCS error during mdrun
Dear GROMACS users, I am trying to run md of a protein with a non-standard residue. It was fine up until I ran mdrun with pr.mdp, where I received a LINCS warning after 20 steps (0.042 ps). Step 21, time 0.042 (ps) LINCS WARNING relative constraint deviation after LINCS: max 236965036032.00 (between atoms 261 and 262) rms 7344678400.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 250252 70.20.1331 0.0388 0.1330 252253 133.70.1000 0.1070 0.1000 252254 113.70.1471 584679.3560 0.1470 254255 99.10.1531 4371462.3199 0.1530 254268 113.20.1531 584679.3412 0.1530 255256 104.00.1531 14918575.9155 0.1530 256257 94.10.1391 71642892.3147 0.1390 256259 118.90.1391 9989150.8212 0.1390 257258 94.70.1090 53680649.8250 0.1090 257261 92.00.1391 165281594.0708 0.1390 259260 167.30.1090 3058365.4015 0.1090 259263 102.70.1391 23632615.9567 0.1390 261262 90.00.1090 25829189100.6878 0.1090 261265 93.50.1391 151539192.8914 0.1390 263264 102.70.1090 23369011.4797 0.1090 263265 99.00.1391 51420376.9215 0.1390 265266 96.00.1361 61029666.4858 0.1360 266267 93.30.1000 22670607.4602 0.1000 268269 123.50.1230 0.1132 0.1230 268270 89.00.1331 0.0916 0.1330 270271 32.20.1000 0.1280 0.1000 270272 32.30.1471 0.1820 0.1470 I looked up the mailing list and found discussion about this subject but there appears to be no conclusions. Any suggestions would be greatly appreciated. Sanghwa Han ___ 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] desort
I have developed a methodology to desort based on the script that I
previously mentioned. The speed of desorting has been improved. For a
system of 100K atoms the setup and processing for mdrun_mpi (grompp's
trjconv's g_desort's etc.) took me 30sec. For a system of 750K atoms the
time was 90sec.
Benifits:
When running in 200ps segments on NP=4 in single precision I get a
speedup of about 1.4 times vs without -shuffle and speedup of 1.15 times
vs. with shuffle but without sort. It is only with sort that my scaling
to NP=4 or NP=16 matches the gromacs benchmarks.
Testing:
1. I have run 20 x 20ps mdrun_mpi iteratively using -shuffle -sort and
this g_desort program and the system looks normal.. no quantitative
test though.
2. I have compared the -deshuf.ndx file produced by grompp to a g_desort
output .ndx file (both produced using -shuffle but not -sort) and they
match exactly.
I have not posted this tool to the uploads section since I don't want
anybody to run into unexpected problems in case it is incorrect since it
affects the mdrun directly.
I welcome any suggestions for ways to test if this is correct. Also, if
anybody has some long-time sorted trajectories out there then they could
use this to recover individual positions and follow their favourite
water molecule. If anybody does do this, please post something about
your success.
This was written from template.c and compilation of this program is done
similarly.
Before using this, please read the static char *desc[] = { completely.
Especially for the warnings that discuss what number your index files
begin with and the exact implementation that is a bit of a hassle based
on the order that grompp does things but it can all be scripted.
Chris Neale.
/*
* $Id: template.c,v 1.4 2001/07/23 15:28:29 lindahl Exp $
*
*This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
*VERSION 3.0
*
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* Do check out http://www.gromacs.org , or mail us at [EMAIL PROTECTED] .
*
* And Hey:
* Gyas ROwers Mature At Cryogenic Speed
*/
/* This line is only for CVS version info */
static char *SRCID_template_c = $Id: template.c,v 1.4 2001/07/23
15:28:29 lindahl Exp $;
#include statutil.h
#include typedefs.h
#include smalloc.h
#include vec.h
#include copyrite.h
#include statutil.h
#include tpxio.h
#include math.h
int main(int argc,char *argv[])
{
static char *desc[] = {
g_desort takes two coordinate files as input and outputs a .ndx
file that ,
can be used to properly sort/shuffle or desort/deshuffle. ,
The -f option takes two coordinate files as input and the order is
important: ,
the first file is the desired order and the second file is the
current order. ,
To desort coordinates g_desort -f unsorted.gro sorted.gro and to
resort ,
coordinates g_desort -f sorted.gro unsorted.gro. In order to use
the -sort option ,
of grompp you will only need to desort your trajectory and g_desort
makes this trivial. ,
However, the benifit of sorting ,
decreases over time as the particles move away from their sorted
positions. Therefore ,
regular re-sorting is desirable. The usage section below describes
how to do this. ,
The basic idea is to pre-sort the .trr file for loading into grompp
based on a resort ,
.ndx file generated by g_desort after a preliminary grompp without
the .trr. An additional ,
sorting step is added to ensure that the grompp sorting did not
change based on the loaded i,
.trr file. The mdrun in then completed and desorted prior to
starting again. \n,
USAGE: \n,
1. grompp -shuffle -sort -c original.gro -o sorted_temp.tpr \n,
2. editconf -f sorted_temp.tpr -o sorted_temp.gro \n,
3. g_desort -f sorted_temp.gro original.gro -o resort_temp.ndx \n,
4. trjconv -f original.trr -n resort_temp.ndx -o sorted.trr \n,
5. grompp -shuffle -sort -c original.gro -t sorted.trr -o
sorted.tpr \n,
6. editconf -f sorted.tpr -o
Re: [gmx-users] MD Error after adding a unnatural amio acid
Hi Tsjerk Wassenaar, I am trying to build a protein with a non-standard amino acid by adding (covalent bond, this is what I mean by linkage ) a bulky group (163 atoms) to the side chain of an existing natural amino acid of wild type protein. Energy minimization of the modified protein had been performed in gas phase and solvent. The solvent and whole system were also minimized and equilibrated at different temperatures before MD simulation. During MD, either the covalent I build or its neighboring one got broken, and the simulation terminated. Minimizations could not had been done if building block is a problem, right? Following is the line in my mdp file: tc-grps = Protein_A ASO_A ASO_B SOL NA CL Thanks, Liu, Yuemin --- Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Liu yuemin, Now I haven't got a clue of what you're trying to do! Okay, add a new group somewhere and do MD... First of all, what is the group you're talking about? How did you link it. You mention the linkage being broken, but you're not doing QM; bonds stay bonds, but may go well out of bounds. Did you perform energy minimization? Did you check the stability of the group alone in solution? You talk about different groups for temperature coupling? Maybe give the tc_coupl related lines from the .mdp files? Note that you shouldn't couple such a group separately. Or do you mean charge groups? Please try to be clear on such things. Anyway, at this point the partial charges seem to be the least of your worries (unless you have a collection of -1,+1 or worse stuck together). I suspect your trouble is related to the building block. Cheers, Tsjerk On 1/24/07, yuemin liu [EMAIL PROTECTED] wrote: Hi Everyone, I once talked about this before and have new problem now. The new group was successfully attached to the protein, but problem comes during the process of MD. The error messages are always like the following with either new linkage broken or a neighboring Hydrogen flying away. Parameters except for partial charge are perfectly okay. The partial charges from HF calculations even made it worse, because of different scheme with gmx. I also tried to partition the new bulky group into small fragments when T-coupling, but did not help. I am wondering what the reasons are. Is the new group too big? What is the alternative to assign partial charge in gmx other than PRODRG? Wishes, Liu, Yuemin Energies (kJ/mol) Bond AngleProper Dih. Improper Dih. LJ-14 4.40414e+037.17452e+033.03251e+03 2.44614e+032.21377e+03 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential 4.01788e+042.57243e+05 -1.94251e+06 -2.87497e+05 -1.91331e+06 Kinetic En. Total EnergyTemperature Pressure (bar) 3.45332e+05 -1.56798e+062.99118e+02 -1.03238e+01 Shake did not converge in 1000 steps i mi j mj before after should be 3173 14.01 3174 1.01 0.1 0.15192 0.1 Constraint error in algorithm Shake at step 650187 Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ 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] MD Error after adding a unnatural amio acid
Hi Everyone, I once talked about this before and have new problem now. The new group was successfully attached to the protein, but problem comes during the process of MD. The error messages are always like the following with either new linkage broken or a neighboring Hydrogen flying away. Parameters except for partial charge are perfectly okay. Well, actually these symptoms would tend to indicate that the new bonding topology is not okay :-) The partial charges from HF calculations even made it worse, because of different scheme with gmx. I also tried to partition the new bulky group into small fragments when T-coupling, but did not help. No, don't do that! In the vast majority of cases, you only want coupling groups for (e.g.) surface, solvent, membrane, solute... not ions or other little bits of stuff. I am wondering what the reasons are. Is the new group too big? What is the alternative to assign partial charge in gmx other than PRODRG? The only reasonable method is to use a method similar to that which designed the partial charges in the original force field, and then to verify that those charges lead to reasonable simulations. Anything else could be just so much fiction :-) I would go back and assemble the topology of this thing piece by piece, verifying at each stage that you have structural integrity... the stepwise process will help you find where the real problem is, if an inspection of the topology doesn't work in the first place! Mark ___ 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
