[gmx-users] Topology and force fields
Hello all, Below are the contents of a water1.top file that I used to simulate 2000 molecules of TIP3P water (NPT). I made this topology file according to the pattern on page 114 of the manual (topology for Urea in water). My diffusion coefficient, viscosity and radial distribution functions matched those for tip3p water in literature. Recently I was told that I did not need to use another force field in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield on its own. Could this be true? I just wanted to verify the authenticity of my simulation. If the structure of the topology below is not correct, please let me know. ; The force field files to be included #include "ffcharmm27.itp" ; Include TIP3P water topology #include "tip3p.itp" [ system ] Pure Water [ molecules ] ;molecule name number SOL 1936 SOL64 I appreciate your answers. Lum -- 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: Parameters for AOT molecule/Too few parameters on line
Justin, I appreciate your reply. Actually, I have read through the section of building parameter files in chap. 5 several times. The only reason for using atom types instead of numbers is because that is the way they are represented in the ffcharmmbon.itp and ffcharmmnb.itp files. Numbers are not used in these force fields. The [ bondtypes ] below is a portion of the [bondtypes ] listed in the ffcharmmbon.itp file. I will definitely use numbers. [ bondtypes ] ; ijfuncb0kb CSTOST10.116784884.928 SSFE10.232209200.0 CC10.1335502080.0 CACA10.1375255224.0 CE1CE110.134368192.0 CE1CE210.1342418400.0 CE1CT210.1502305432.0 Thank you, Lum > Lum Nforbi wrote: > > Hello all, > > > > I have built a parameter file for the AOT surfactant molecule and > > tried to minimize the energy of a mixture of several of this molecule > > and water molecules but I have the warnings at the bottom part of this > > mail. Gromacs basically goes through all the lines of parameters > > starting from [ bonds ] and says the parameters are too few. I am also > > using the charmm force field. > > > > Here is the way I constructed the aot.itp parameter file. I am not > > sure this is correct. Excerpts of the parameter file are belowl. > > > > - I drew the AOT molecule and did the bond and angle connections in the > > molecule.The atom names are provided by the ffcharmm27.atp file. All > > The .atp file contains atom types, not atom names. Your [bonds], [angles], > etc. > should be numbers, not atom types or names. For instance, if atoms 1 and > 2 > are bonded: > > [ bonds ] > 12(function type, etc) > values are obtained from the ffcharmmbon.itp file and ffcharmmnb.itp file. > > - I am not sure how to build the dihedrals since the are X's in the [ > > dihedrals ] section of the ffcharmmbon.itp file. > > > > As Mark indicated earlier, an X is simply a wildcard - it can correspond to > any > number of atom types. > > > My question is: Why does the program say I have few parameters while I > > just out together parameters from the charmm27 force field? Please, if I > > am doing something wrong, can someone let me know? > > [ bonds ] > > ; ijfuncb0kb > > SLO2L10.1448451872.0 > > You're using either atom types or names in these sections, which is > completely > incorrect. Please have a thorough read through Chapter 5 of the manual. > > > > > NOTE 1 [file aotwater.top, line 19]: > > System has non-zero total charge: -1.35e+01 > > > > I would also be *very* concerned about this line. You have a negative > charge of > -13.5, indicating that whatever charges you've assigned to your small > molecule > have left a fractional charge on the system, which is clearly non-physical. > > -Justin > > > processing coordinates... > > double-checking input for internal consistency... > > renumbering atomtypes... > > converting bonded parameters... > > initialising group options... > > processing index file... > > Analysing residue names: > > Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat > > There are:60 OTHER residues > > There are: 0PROTEIN residues > > There are: 0DNA residues > > Analysing Other... > > Making dummy/rest group for T-Coupling containing 1110 elements > > Making dummy/rest group for Acceleration containing 1110 elements > > Making dummy/rest group for Freeze containing 1110 elements > > Making dummy/rest group for Energy Mon. containing 1110 elements > > Making dummy/rest group for VCM containing 1110 elements > > Number of degrees of freedom in T-Coupling group rest is 3192.00 > > Making dummy/rest group for User1 containing 1110 elements > > Making dummy/rest group for User2 containing 1110 elements > > Making dummy/rest group for XTC containing 1110 elements > > Making dummy/rest group for Or. Res. Fit containing 1110 elements > > Making dummy/rest group for QMMM containing 1110 elements > > T-Coupling has 1 element(s): rest > > Energy Mon. has 1 element(s): rest > > Acceleration has 1 element(s): rest > > Freeze has 1 element(s): rest > > User1has 1 element(s): rest > > User2has 1 element(s): rest > > VCM has 1 element(s): rest > > XTC has 1 element(s): rest > > Or. Res. Fit has 1 element(s): rest > > QMMM has 1 element(s): rest > > Ch
[gmx-users] Parameters for AOT molecule/Too few parameters on line
Hello all, I have built a parameter file for the AOT surfactant molecule and tried to minimize the energy of a mixture of several of this molecule and water molecules but I have the warnings at the bottom part of this mail. Gromacs basically goes through all the lines of parameters starting from [ bonds ] and says the parameters are too few. I am also using the charmm force field. Here is the way I constructed the aot.itp parameter file. I am not sure this is correct. Excerpts of the parameter file are belowl. - I drew the AOT molecule and did the bond and angle connections in the molecule.The atom names are provided by the ffcharmm27.atp file. All values are obtained from the ffcharmmbon.itp file and ffcharmmnb.itp file. - I am not sure how to build the dihedrals since the are X's in the [ dihedrals ] section of the ffcharmmbon.itp file. My question is: Why does the program say I have few parameters while I just out together parameters from the charmm27 force field? Please, if I am doing something wrong, can someone let me know? [ bonds ] ; ijfuncb0kb SLO2L10.1448451872.0 SL CTL11 0.1800 376560.0 CTL1HAL110.258571.2 [ angles ] ; ijkfuncth0cthub0cub 02L SL O2L 5 109.471087.840.24529288.0 O2L SL CTL15 98.0711.280.00.0 SL CTL1HAL15 110.10288.6960.217918853.104 [ dihedrals ] ; ijklfuncphi0cpmult HAL1CTL1SLO2L90.000.03 CTL2OSLSLO2L90.000.03 CLCTL1SLO2L90.000.03 XCTL1CTL2X90.000.83683 XCTL1CTL2X90.000.83683 [ atoms ] ;nameat.nummasschargeptypesigmaepsilon CL612.011000.62A0.3563594872560.29288 HAL111.0080000.09A0.2351972615890.092048 HAL211.0080000.09A0.2387608564620.117152 [ pairs ] ; ijfuncsigma1-4epsilon1-4 ; THESE ARE 1-4 INTERACTIONS CTL1CTL110.3385415128930.04184 CTL1CTL210.3385415128930.04184 CTL1CTL310.3385415128930.04184 WARNING 141 [file aot_2.itp, line 228]: Too few parameters on line (source file toppush.c, line 1248) WARNING 142 [file aot_2.itp, line 229]: Too few parameters on line (source file toppush.c, line 1248) Excluding 3 bonded neighbours molecule type 'AOT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file aotwater.top, line 19]: System has non-zero total charge: -1.35e+01 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are:60 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Making dummy/rest group for T-Coupling containing 1110 elements Making dummy/rest group for Acceleration containing 1110 elements Making dummy/rest group for Freeze containing 1110 elements Making dummy/rest group for Energy Mon. containing 1110 elements Making dummy/rest group for VCM containing 1110 elements Number of degrees of freedom in T-Coupling group rest is 3192.00 Making dummy/rest group for User1 containing 1110 elements Making dummy/rest group for User2 containing 1110 elements Making dummy/rest group for XTC containing 1110 elements Making dummy/rest group for Or. Res. Fit containing 1110 elements Making dummy/rest group for QMMM containing 1110 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... NOTE 2 [file aotwater_min.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 1 Mb of data writing run input file... There were 2 notes There were 142 warnings --- Program grompp, VERSION 4.0.5 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (142), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. --- I appreciate your answers. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv
[gmx-users] X's in the ffcharmm27bon.itp force field
Hello all, Please, can someone let me know why there are X's in the [dihedraltypes] section of the ffcharmm27bon.itp force field and what they actually stand for? Could they be replaced with actual atoms or no? I appreciate your replies. Lum -- 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: How to include sodium ion (Reply to Justin's mail)
Justin, The sodium ion I am talking about is part of the docusate sodium salt (AOT). If I want to solvate 100 AOT molecules with water molecules, how do I make sodium ions part of the system? I am not just adding sodium ions to balance the charge of the system. The sodium ions are part of the AOT molecules, so I need 100 sodium ions in the system. Do I just add one sodium ion in the parameter file containing the rest of the 65 atoms of AOT, then specify #include "ions.itp" in the fopology? I appreciate your answers. (Aside: Can you help with replying emails via this forum. I use gmail and when I click the reply tab, it includes all the mails for that issue, and there is no "subject" entry. So I always have to copy and paste the mail before replying. I appreciate your help). Lum Nforbi wrote: > Hi All, > >I would like to include sodium ions into a water/AOT (sodium > di-2-ethylhexylsulfoccinate) cubic box. Can someone tell me how to do > this and how to include parameters for the sodium ion in the parameter file? > I appreciate your answers. Shouldn't this be as simple as using genion and then: #include "ions.itp" in the topology? Or is there some other problem you're having? -Justin > > Lum > -- 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] How to include sodium ion
Hi All, I would like to include sodium ions into a water/AOT (sodium di-2-ethylhexylsulfoccinate) cubic box. Can someone tell me how to do this and how to include parameters for the sodium ion in the parameter file? I appreciate your answers. Lum -- 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: Choice of value of rlist, rvdw and rcoulomb
Dear Mark and Amit, I appreciate your replies. I have read this portion of the gromacs manual which talks about cut-offs, but I don't clearly understand the physical significance of the choice of values. I am using for my experiments vdwtype = cutoff, which is twin-range cut-off with rlist = neighbour list cut off and rvdw = vdw cut-off where rvdw >= rlist. I have run three different experiments (NPT simulation of 200 particles of oxygen at 80K ie liquid oxygen) but with different rlist and rvdw values to evaluate the influence of these values on my Lennard-Jones plots. The literature Lennard-Jones parameters for oxygen which I have been using are epsilon = 0.939482 KJ/mol and sigma = 0.3433 nm. The book "Computer Simulation of Liquids" by Allen and Tildesley recommends the use of rvdw = 2.5xsigma. In my case, if I use this recommendation, my rvdw value would be 0.86. The values I have used and the results are as follows: RLIST = 0.3, RVDW = 0.7 RESULT: RDF Plot converges to 1 (WORKS). RLIST = 0.3, RVDW = 1.0 RESULT: RDF Plot converges to 0 after third peak (DOES NOT WORK). RLIST = 0.7, RVDW = 0.7 RESULT: RDF Plot converges to 0 after third peak (DOES NOT WORK). I know that the problem is not about equilibration, because the first experiment which worked did not even equilibrate fully but gave the right plot. My question is: what is the physical significance of choosing these values? I know that rlist is used as cut-off for neighbour list generation and to specify which atom pairs are interacting, so that these interactions can be calculated at every step of the simulation. rvdw specifies the radius of atoms which will interact in a vdw manner. Why would a rvdw = 0.7 work and rvdw = 1.0 not work looking at a system in a physical sense? 0.7 and 1.0 are both close to the recommended 0.86 value for rvdw, so why does one work and not other? What could be happening in the system? If I don't understand physically what these values really mean, I may never fully grasp what is going on in the system. Please help me out. The .mdp file I have used below is the same in all three cases, the only modifications being the rlist and rvdw values. integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 50 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 1000 ; freq. x_out nstvout = 1000 ; freq. v_out nstfout = 0 ; freq. f_out nstlog = 100 ; energies to log file nstenergy= 100 ; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist= 0.3; cut-off distance for the short range neighbour list pbc = xyz; Periodic boundary conditions:xyz, use periodic boundary conditions in all directions periodic_molecules = no ; molecules are finite, fast molecular pbc can be used vdw-type = Cut-off; van der Waals interactions rvdw = 0.7; distance for the LJ or Buckingham cut-off fourierspacing = 0.135 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order= 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = v-rescale ; temp. coupling with vel. rescaling with a stochastic term. tau_t= 0.1; time constant for coupling tc-grps = OXY; groups to couple separately to temp. bath ref_t= 80 ; ref. temp. for coupling Pcoupl = berendsen ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p= 0.5; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p= 1.0; ref. pressure for coupling (bar) gen_vel = yes; generate velocities according to a Maxwell distr. at gen_temp gen_temp = 80 ; temperature f
[gmx-users] Choice of value of rlist, rvdw and rcoulomb
Hi all, Please, can someone let me know if the choice of the value of rlist, rvdw and rcoulomb is related to or depends in someway to the distance between atoms on a lennard-jones potential plot? I appreciate your answers. Lum -- 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] Cut-offs in gromacs
Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both systems below. The barostats are different but I don't think this is the cause. I think that one worked because of the cut-off specifications (rlist, rvdw and rcoulomb), but I am not sure of the explanation of how the cut-off values can influence the shape of a pair distribution function. The fourier spacing in both parameter files are also different. Please, if someone knows how these cut-off values and maybe fourier spacing could influence the shape of a pair distribution function, let me know the explanation. .mdp file which gave the plot which converges to zero: title= NPT simulation of a LJ FLUID cpp = /lib/cpp include = -I../top define = integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 50 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 500; freq. x_out nstvout = 500; freq. v_out nstfout = 0 ; freq. f_out nstlog = 50 ; energies to log file nstenergy= 50 ; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist= 1.0; cut-off distance for the short range neighbour list pbc = xyz; Periodic boundary conditions:xyz, use periodic boundary conditions in all directions periodic_molecules = no ; molecules are finite, fast molecular pbc can be used coulombtype = PME; particle-mesh-ewald electrostatics rcoulomb = 1.0; distance for the coulomb cut-off vdw-type = Cut-off; van der Waals interactions rvdw = 1.0; distance for the LJ or Buckingham cut-off fourierspacing = 0.12 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order= 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = v-rescale ; temp. coupling with vel. rescaling with a stochastic term. tau_t= 0.1; time constant for coupling tc-grps = OXY; groups to couple separately to temp. bath ref_t= 80 ; ref. temp. for coupling Pcoupl = berendsen ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p= 0.5; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p= 1.0; ref. pressure for coupling (bar) gen_vel = yes; generate velocities according to a Maxwell distr. at gen_temp gen_temp = 80 ; temperature for Maxwell distribution gen_seed = 173529 ; used to initialize random generator for random velocities .mdp file which gave the plot which converges to 1: title= NPT simulation of a LJ FLUID cpp = /lib/cpp include = -I../top define = integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002; time-step in ps nsteps = 50 ; total number of steps; total time (1 ns) nstcomm = 1; frequency for com removal nstxout = 1000 ; freq. x_out nstvout = 1000 ; freq. v_out nstfout = 0; freq. f_out nstlog = 500 ; energies to log file nstenergy= 500 ; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = g
Re: [gmx-users] Restarting mdrun
Hi Chadan, I have used the two commands below to CONTINUE a run and they worked fine for me. I am also using gromacs-4.0.5. tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e wfullmdrun_ener.edr -g md.log -cpi state_prev.cpt -append & The first command includes the amount of time by which you want to extend your run. The second one just appends the results to your existing files. In this second command, you are using the new .tpr file you created in the first command. Use the state.cpt file instead of the state_prev.cpt file in order to avoid losing time. Hope this helps. Lum On 17/02/10 02:52, Chandan Choudhury wrote: > Hello gmxusers !!! > I want to continue my simulation, from where the point where it stopped. > The gmxcheck on .trr and cpt files are as: > > $gmxcheck -f state.cpt > > Checking file state.cpt > > # Atoms 186864 > Last frame -1 time 9362.500 > > > Item#frames Timestep (ps) > Step 1 > Time 1 > Lambda 1 > Coords 1 > Velocities 1 > Forces 0 > Box 1 > > $gmxcheck -f 5-10.trr > > Checking file 5-10.trr > trn version: GMX_trn_file (single precision) > Reading frame 0 time 5169.500 > # Atoms 186864 > Reading frame8000 time 9169.500 > > > Item#frames Timestep (ps) > Step 83950.5 > Time 83950.5 > Lambda83950.5 > Coords83950.5 > Velocities83950.5 > Forces 0 > Box 83950.5 > > > There is a mismatch of time in both the outputs. > > The date of modification of both the files as shown are: > > Feb 15 19:55 state.cpt > > $date -r 5-10.trr > Mon Feb 15 19:59:56 IST 2010 > > The cpt file shows time greater than the trr file. But the time of > modification of cpt file is less than trr file. If the simulation stopped catastrophically, then the timestamp could easily differ, especially if the .cpt is opened, written to and closed periodically, and the .trr is open continuously. > Cannot understand the, > how to restart the mdrun. And the size of the trr file is 36GB. Can I > use the append flag in mdrun for gmx 4.0.5. Search the webpage for suggestions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Working with Reduced Units
Hi all, Please, can someone shed more light on how to set up reduced units in an .mdp file? I have tried to this but it does not work. I set epsilon, sigma and mass to 1 in my force field file as stated in section 2.3 of the manual. I multiplied 300K temperature by 0.00831451 and divided by epsilon to get a temperature in reduced units with value 2.5. I also calculated the pressure of 1bar in reduced units as shown on Table 2.4 of the manual to get a value of 0.0431 and included all of these in the .mdp file but this did not work for me in the mdrun. Is this the right way to set up reduced units in gromacs? Please, help me out. Thanks, Lum -- 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: Number of grid cells is zero. Probably the system and box collapsed.
Hello all, After minimizing the energy of my system of 200 particle coordinates of box dimension 3.5 nm to an acceptable value, I proceeded to doing mdrun but got the error message: "Source code file: nsgrid.c, line: 348. Fatal error: Number of grid cells is zero. Probably the system and box collapsed." I was wondering what could be the cause. Below are my energy minimization parameter file, the results of the minimization and the mdrun parameter file. oxymin.mdp file title= NPT simulation of a Lennard-Jones Fluid cpp = /lib/cpp include = -I../top define = constraints = none integrator = steep nsteps = 5000 emtol= 1000 emstep = 0.10 nstlist = 10 rlist= 0.9 ns_type = grid coulombtype = PME rcoulomb = 0.9 vdwtype = cut-off rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 optimize_fft = yes Step= 673, Dmax= 6.9e-03 nm, Epot= 6.11020e+05 Fmax= 7.64685e+03, atom= 19 Step= 675, Dmax= 4.1e-03 nm, Epot= 6.10956e+05 Fmax= 1.71624e+03, atom= 53 Step= 677, Dmax= 2.5e-03 nm, Epot= 6.10933e+05 Fmax= 3.60118e+03, atom= 30 Step= 678, Dmax= 3.0e-03 nm, Epot= 6.10927e+05 Fmax= 3.03499e+03, atom= 19 Step= 679, Dmax= 3.6e-03 nm, Epot= 6.10915e+05 Fmax= 4.80541e+03, atom= 30 Step= 680, Dmax= 4.3e-03 nm, Epot= 6.10913e+05 Fmax= 4.79865e+03, atom= 19 Step= 681, Dmax= 5.2e-03 nm, Epot= 6.10910e+05 Fmax= 6.50875e+03, atom= 30 Step= 683, Dmax= 3.1e-03 nm, Epot= 6.10857e+05 Fmax= 9.58182e+02, atom= 160 writing lowest energy coordinates. Back Off! I just backed up oxymin.gro to ./#oxymin.gro.6# Steepest Descents converged to Fmax < 1000 in 684 steps Potential Energy = 6.1085662e+05 Maximum force = 9.5818250e+02 on atom 160 Norm of force = 2.9207101e+02 oxymdrun.mdp file title= NPT simulation of a LJ FLUID cpp = /lib/cpp include = -I../top define = integrator = md ; a leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 ; time-step in ps nsteps = 50 ; total number of steps; total time (1 ns) nstcomm = 1 ; frequency for com removal nstxout = 1000 ; freq. x_out nstvout = 1000 ; freq. v_out nstfout = 0 ; freq. f_out nstlog = 500; energies to log file nstenergy= 500; energies to energy file nstlist = 10 ; frequency to update neighbour list ns_type = grid ; neighbour searching type rlist= 0.9; cut-off distance for the short range neighbour list coulombtype = PME; particle-mesh-ewald electrostatics rcoulomb = 0.9; distance for the coulomb cut-off vdw-type = Cut-off; van der Waals interactions rvdw = 0.9; distance for the LJ or Buckingham cut-off fourierspacing = 0.12 ; max. grid spacing for the FFT grid for PME fourier_nx = 0 ; highest magnitude in reciprocal space when using Ewald fourier_ny = 0 ; highest magnitude in reciprocal space when using Ewald fourier_nz = 0 ; highest magnitude in reciprocal space when using Ewald pme_order= 4 ; cubic interpolation order for PME ewald_rtol = 1e-5 ; relative strength of the Ewald-shifted direct potential optimize_fft = yes; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = nose-hoover; temp. coupling with vel. rescaling with a stochastic term. tau_t= 0.5; time constant for coupling tc-grps = OXY; groups to couple separately to temp. bath ref_t= 80 ; ref. temp. for coupling Pcoupl = parrinello-rahman ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p= 0.9; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p= 1.0; ref. pressure for coupling (bar) gen_vel = yes; generate velocities according to a Maxwell distr. at gen_temp gen_temp
[gmx-users] Re: Lennard-Jones Rdf plot
gth of the Ewald-shifted direct potential optimize_fft = yes; calculate optimal FFT plan for the grid at start up. DispCorr = no ; Tcoupl = v-rescale ; temp. coupling with vel. rescaling with a stochastic term. tau_t= 0.1; time constant for coupling tc-grps = OXY; groups to couple separately to temp. bath ref_t= 80 ; ref. temp. for coupling Pcoupl = berendsen ; exponential relaxation pressure coupling (box is scaled every timestep) Pcoupltype = isotropic ; box expands or contracts evenly in all directions (xyz) to maintain proper pressure tau_p= 0.5; time constant for coupling (ps) compressibility = 4.5e-5 ; compressibility of solvent used in simulation ref_p= 1.0; ref. pressure for coupling (bar) gen_vel = yes; generate velocities according to a Maxwell distr. at gen_temp gen_temp = 300.0 ; temperature for Maxwell distribution gen_seed = 173529 ; used to initialize random generator for random velocities (5) Results at the end of the simulation Statistics over 501 steps [ 0. thru 1. ps ], 7 data sets All averages are exact over 501 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -1044.9722.946822.7766 -0.000966612 -9.66612 Kinetic En. 198.35411.428211.4279 -3.0823e-05 -0.30823 Total Energy-846.6225.819425.6583 -0.000997435 -9.97435 Temperature 79.92084.604674.60453 -1.24192e-05 -0.124192 Pressure (bar) 0.278412 89.84289.8327 0.000447827 4.47828 Volume 10.07190.42992 0.426807 -1.78902e-05 -0.178902 Density (SI)528.13413.669813.5568 0.000607606 6.07606 Heat Capacity Cv: 12.5342 J/mol K (factor = 0.00331954) Isothermal Compressibility: 0.0016631 /bar Adiabatic bulk modulus:601.288 bar (6) I then plotted a Potential Energy graph and a radial distribution function for the system at the end of the simulation. I have attached the graphs. The commands for g_rdf are below: make_ndx -f oxymdrun.gro -o oxy.ndx trjconv -f oxymdrun_traj.trr -o oxymdrun_traj.xtc g_rdf -f oxymdrun_traj.xtc -n oxy.ndx -o oxy_rdf.xvg Select a reference group and 1 group Group 0 ( System) has 200 elements Group 1 ( OXY) has 200 elements Select a group: 1 Selected 1: 'OXY' Select a group: 1 Selected 1: 'OXY' Last frame 1 time 1.000 The first two peaks on the radial distribution function plot are ok, but the third one starts slanting down ie it does not converge to 1.0. I am not sure what I am not setting right and I don't know what could be the cause of the graph slanting downwards. In section 2.3 of page 9 of the manual, it is mentioned that reduced units are good for simulating LJ systems, but Gromacs already has a fixed set units that it uses and I am not sure how to set the reduced units such that Gromacs can recognize them. Could it be a reduced units problem? I appreciate your answers. Lum - Show quoted text - Lum Nforbi wrote: > Dear all, > >Please, could someone tell me what could be the problem with the > attached LJ plot? > Could it be due to wrong assignment of periodic boundary conditions? > First, do not attach files without file extensions. For those of us who are security-conscious (some say "paranoid"), we won't open it. It is much more useful to post an image file to some public site, like Photobucket or Google Docs. Second, there is likely no way anyone can diagnose your problem unless you post a very detailed description of what you're doing. You mention an "LJ plot" but the file name of your attachment would suggest a radial distribution function. What is it that you are trying to analyze? How did you produce the plot? Is it indeed an RDF? If so, what was simulated, and for how long? What were your .mdp parameters? It is very doubtful that PBC alone caused issues, but rather your incorrect assignment of, e.g., cutoffs or some other feature. But we don't know any of this yet. Remember, we can't get inside your head to know what you're doing. You've got to make it easy for us. -Justin > Thank you, > Lum > RDF_oxyoxy.agr Description: application/grace -- 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] Lennard-Jones Rdf plot
Dear all, Please, could someone tell me what could be the problem with the attached LJ plot? Could it be due to wrong assignment of periodic boundary conditions? Thank you, Lum RDF_oxyxoy Description: Binary data -- 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] Genbox error message
Hello all, Can someone tell me the meaning of this error message after using the genbox command? *** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7e7c454] genbox[0x81195c4] === Memory map: 08048000-082be000 r-xp 08:01 4333977 /usr/local/gromacs/bin/genbox 082be000-082bf000 r-xp 00275000 08:01 4333977 /usr/local/gromacs/bin/genbox 082bf000-082c5000 rwxp 00276000 08:01 4333977 /usr/local/gromacs/bin/genbox 082c5000-082cb000 rwxp 082c5000 00:00 0 0958f000-099e9000 rwxp 0958f000 00:00 0 [heap] b7df3000-b7df4000 rwxp b7df3000 00:00 0 b7df4000-b7e09000 r-xp 08:01 3860700/lib/tls/i686/cmov/ libpthread-2.8.90.so b7e09000-b7e0a000 r-xp 00014000 08:01 3860700/lib/tls/i686/cmov/ libpthread-2.8.90.so b7e0a000-b7e0b000 rwxp 00015000 08:01 3860700/lib/tls/i686/cmov/ libpthread-2.8.90.so Aborted I appreciate your help. Lum -- 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] Gromacs 4.1
Hi Mark, When will Gromacs 4.1 be available? Thank you, Lum -- 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] Simulation with Implicit solvents
Hello all, Has anyone done simulation with implicit solvents? If so, please, could you let me know how implicit solvents are set up, in general? Is there some documentation where I could find this information in? Thank you, Lum -- 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: Opening .o files - in response to Erik's question.
Thanks to Tsjerk, David and Erik for replying. This is in response to Erik's question on what is it I intend to do exactly. I would like to view the source code for g_energy so that I can see what formula was used to calculate Cp as well as viscosity (obtained when the -vis option is used). I opened gmx_energy.c using gromacs-4.0.5/src/tools$ more gmx_energy.c and found a code which I think is the source code, but it is quite difficult to comprehend. I guess this code is written in the c++ language, which I am unfamiliar with, so I wanted to see if there was something else that had an easier-to-understand code and that's why I tried opening the g_energy.o file. This may be dumb but I am not quite used to the files and I will eventually get it. If the gmx_energy.c file is the source code, is there a way convert it into, for example, fortran? Thank you, Lum > Lum Nforbi wrote: >> Dear all, >> >>I am having problems opening the g_energy.o file in the >> gromacs-4.0.5 folder. Can someone tell me how to open this file? What >> is the general way of opening .o files? >> >> Thank you, >> Lum >> > this is an intermediate file from the compiler. You do not need to > open it at any time. > That's not entirely true. I've inspected .o-files at times to find the reason for certain linker problems. 'objdump', 'readelf' and 'nm' are examples of linux tools that can extract information form .o-files. Nevertheless, inspecting such files is only useful in very special situations. What is it that you intend to do exactly? -- 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] Opening .o files
Dear all, I am having problems opening the g_energy.o file in the gromacs-4.0.5 folder. Can someone tell me how to open this file? What is the general way of opening .o files? Thank you, Lum -- 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] Viscosity determination
Dear all, Below is my output for viscosity determination. In order to get a value for the viscosity, do I just take an average of the numbers in the third column? # This file was created Wed Jan 6 16:25:24 2010 # by the following command: # g_energy -f wfullmdrun_ener.edr -vis viscosity.xvg # # g_energy is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title "Bulk Viscosity" @xaxis label "Time (ps)" @yaxis label "\8h\4 (cp)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Shear" @ s1 legend "Bulk" 0.150.8340840.546697 0.30.883405 0.51992 0.5999850.9052920.495556 0.799980.9139110.470734 0.750.9151440.452457 1.199970.9151210.438746 1.399970.9171060.430864 1.599960.9200710.418252 1.799960.9217770.403171 1.50.9189830.394725 2.199950.9181220.387048 2.399940.9233320.383686 Thank you, Lum -- 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] Problems with calculating Cv and Cp
> > Hi Andrew Paluch, > You had asked me to supply the formulas that I attempted using to calculate Cv. The formula from J. M. Haile is labelled isometric heat capacity and given by Cv = Nk/(N-NT*(3(N/2)-1)) and the one in Allen and Tildesley is quite complicated to write out (has some special characters in it). I also found in one of the volumes of gmx-users where someone had used the formula Cv = 1/(k_B*T*T)*Var(E) and instead of having the expected 75 J/Kmol, he got 86 J/Kmol. He also mentioned that Var(E) can be obtained from RMSD numbers. I know that RMSD numbers are displayed from g_energy, but how do you get Var(E) from these numbers? Thanks, Lum > > Date: Wed, 9 Dec 2009 20:45:57 -0500 > From: Andrew Paluch > Subject: Re: [gmx-users] Problems with calculating Cv and Cp > To: Discussion list for GROMACS users > Message-ID: <8be66d7c-ea0f-4b04-8dde-374529ec2...@nd.edu> > Content-Type: text/plain; charset="us-ascii" > > Lum, > > You'll have better luck if you perform a few simulations at different > temperatures at the same pressure and mole number, and then > numerically differentiate the resulting enthalpy. I believe that the > default heat capacity that Gromacs will print out is only valid for > NVE simulations, and I am not sure of the formulas that you are > referring to from Allen and Tildesley & J.M. Haile. Also, don't > expect your calculated heat capacity with TIP3P to agree the > experimental value. You should under-predict the experimental value. > > Lastly, depending on what you are interested in, you may have better > luck with a water model other than TIP3P. > > Hope this helps, > > Andrew > ___ > ___ > Andrew Paluch > Department of Chemical and Biomolecular Engineering > University of Notre Dame du Lac > apal...@nd.edu > ___ > ___ > > On Dec 9, 2009, at 8:18 PM, Lum Nforbi wrote: > > > Dear all, > > > > I have run an 8 ns NPT simulation of 2000 molecules of TIP3P > > water and I have a very low Cv value of 12.4748 J/mol K (factor = > > 0.000164481). The result is below. I ignored this value and have > > tried using formulas for Cv that I found in the two books: Allen > > and Tildesley & J. M. Haile but I can't come out with the right > > answer. > > Has anyone ever calculated Cv or Cp for water manually from > > scratch and gotten the right answer? If so, please, could you give > > me the details of what you did? > > > > Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data > > sets > > All averages are exact over 401 steps > > > > Energy Average RMSD Fluct. > > Drift Tot-Drift > > -- > > - > > Potential -79498.8285.331285.331 > > 0.000110205 0.881641 > > Kinetic En. 14960.5191.868191.854 > > -0.0010135 -8.10799 > > Total Energy -64538.3353.238353.232 > > -0.000903288 -7.22631 > > Temperature 299.9623.847023.84673 > > -2.0321e-05 -0.162568 > > Pressure (bar) 0.945534194.613194.613 > > 0.0001642811.31425 > > Box-X 3.94528 0.00514348 0.00514348 > > 0 0 > > Box-Y 3.94528 0.00514348 0.00514348 > > 0 0 > > Box-Z 3.94528 0.00514348 0.00514348 > > 0 0 > > Volume 61.4097 0.2403250.24032 > > 6.42593e-07 0.00514075 > > Density (SI) 974.33.806293.80622 > > -1.04747e-05 -0.0837974 > > Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) > > Isothermal Compressibility: 2.27095e-05 /bar > > Adiabatic bulk modulus:44034.4 bar > > > > > > Thank you, > > > > Lum > > > > -- > -- 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] Calculation of Cp
Dear All, I have been struggling with this for over a month now and I have still not been able to figure out how to calculate the Cp of my system of 2000 molecules of water on which I did an NPT simulation. The g_energy command of my system gives a wrong Cv (~12.4749 J/mol.K), which therefore cannot be used to calculate the correct Cp. Can someone explain to me or give me hints on how to calculate the Cp of an NPT simulation of TIP3P water, please? Thank you, Lum -- 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] Fwd: What could be wrong with rdf plot?
-- Forwarded message -- From: Lum Nforbi Date: Thu, Dec 31, 2009 at 12:33 PM Subject: What could be wrong with rdf plot? To: gmx-users@gromacs.org Dear all, I am currently analyzing a system of 2000 molecules of TIP3P water on which I performed a NPT simulation. The plot for g(OO) looks very good but for some reason unknown to me, on the g(OH) plot there is an intense peak coming before the normal peaks that are characteristic of a g(OH) plot. Could someone tell me what is going on? I have attached the graphs for gOO and gOH for viewing. Also, I have still not been able to figure out how to calculate the Cp of my system and I have been struggling with this for over a month now. g_energy for my system gives a wrong Cv (~12). Can someone explain to me or give me hints on how to calculate the Cp of an NPT simulation of TIP3P water, please? Have a wonderful New Year 2010 and Decade (2010-2019)! Thank you, Lum RDF_OWHW1HW2_0_8000PS Description: Binary data -- 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] Using GENCONF
Hi all, Is there a way to use genconf such that it does not reproduce the exact same coordinates over and over again (or multiples of the same coordinates) but assigns different coordinate values to each atom in the x, y and z directions? Thanks, Lum -- 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] Problems with calculating Cv and Cp
Dear all, I have run an 8 ns NPT simulation of 2000 molecules of TIP3P water and I have a very low Cv value of 12.4748 J/mol K (factor = 0.000164481). The result is below. I ignored this value and have tried using formulas for Cv that I found in the two books: Allen and Tildesley & J. M. Haile but I can't come out with the right answer. Has anyone ever calculated Cv or Cp for water manually from scratch and gotten the right answer? If so, please, could you give me the details of what you did? Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift -- - Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.000164281 1.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thank you, Lum -- 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: RDF plot. This is weird!
Hi Justin, I chose my whole system of 2000 water molecules. I discussed this plot with someone and they said that rdf can be plotted for atoms as well as whole molecules and that the shape of my rdf plot was not a problem of my having used the whole system (I am not really sure about this). The length of my run was 8 ns (8000 ps). The energy values don't change much so I think the system is pretty equilibrated. I have included below the results of my last two run continuations of 2000 ps each (I had to extend the run to ensure equlibration): For the extension from 4000 ps to 6000 ps, I have the results, Statistics over 301 steps [ 0. thru 6000.0005 ps ], 10 data sets All averages are exact over 301 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -79499.3288.958 288.95 -0.00126651 -7.59903 Kinetic En. 14960.4 192.23192.206 -0.00176262 -10.5757 Total Energy -64538.9357.576357.538 -0.00302911 -18.1747 Temperature 299.9613.854273.85379 -3.5341e-05 -0.212046 Pressure (bar) 0.925645194.462194.455 0.000953178 5.71907 Box-X 3.94525 0.00514608 0.00514608 0 0 Box-Y 3.94525 0.00514608 0.00514608 0 0 Box-Z 3.94525 0.00514608 0.00514608 0 0 Volume 61.4083 0.240493 0.240493 -3.12077e-07 -0.00187246 Density (SI)974.322 3.80683.80679 4.31424e-06 0.0258854 Heat Capacity Cv: 12.4749 J/mol K (factor = 0.000165103) Isothermal Compressibility: 2.2742e-05 /bar Adiabatic bulk modulus:43971.6 bar For extension from 6000 ps to 8000 ps, the results are: Statistics over 401 steps [ 0. thru 8000.0005 ps ], 10 data sets All averages are exact over 401 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -79498.8285.331285.331 0.000110205 0.881641 Kinetic En. 14960.5191.868191.854 -0.0010135 -8.10799 Total Energy -64538.3353.238353.232 -0.000903288 -7.22631 Temperature 299.9623.847023.84673 -2.0321e-05 -0.162568 Pressure (bar) 0.945534194.613194.613 0.000164281 1.31425 Box-X 3.94528 0.00514348 0.00514348 0 0 Box-Y 3.94528 0.00514348 0.00514348 0 0 Box-Z 3.94528 0.00514348 0.00514348 0 0 Volume 61.4097 0.2403250.24032 6.42593e-07 0.00514075 Density (SI) 974.33.806293.80622 -1.04747e-05 -0.0837974 Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481) Isothermal Compressibility: 2.27095e-05 /bar Adiabatic bulk modulus:44034.4 bar Thanks, Lum -- 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] Fwd: RDF plot. This is weird!
Hi, I am forwarding the message and the attachment because I did not see my message in the inbox of gmx-users; I saw only the attached file. Please, can the text be included? Thank you. -- Forwarded message -- From: Lum Nforbi Date: Wed, Dec 9, 2009 at 11:59 AM Subject: RDF plot. This is weird! To: gmx-users@gromacs.org Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1h 45 min to be complete. The plot does not follow the normal trend I see for rdf plot ie first peak higher than the second, so I know something is wrong but I don't know what. Can someone take a look at my graph and tell me what is wrong with my system or with my computation? Thank you, Lum RDF_SOLSOL Description: Binary data -- 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] RDF plot. This is weird!
Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1h 45 min to be complete. The plot does not follow the normal trend I see for rdf plot ie first peak higher than the second, so I know something is wrong but I don't know what. Can someone take a look at my graph and tell me what is wrong with my system or with my computation? Thank you, Lum RDF_SOLSOL Description: Binary data -- 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] To continue a run
Hello all, I am a little confused with this. Which of these 2 files is used when continuing a run: state.cpt or state_prev.cpt? These are binary files. Is there a way to view them? Thank you, Lum -- 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] Radial distribution specifications
Dear all, I need to plot the radial distribution functions but I am not sure how you specified the different radial pair distribution functions for H2O: gOO, gOH and gHH, in order to have different plots. Please, can you help me out with this? Thank you, Lum -- 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] How to plot Pressure (bar) vs simulation time in ps
Hi everyone, I need to plot a graph of pressure (bar) vs run time (ps) but I am havin problems with this because the graph's y-axis diplays energy (KJmol^-1) instead of pressure. How can I correct this energy on the y-axiz of my plot to pressure (bar)? I have used this command to view the value of my pressure (g_energy -f wfullmdrun_ener.edr -o wfullmdrun_PRESSURE4000ps.xvg) and I choose the pressure in the table below in order to display the value. Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. --- 1 LJ-(SR) 2 Coulomb-(SR) 3 Coul.-recip. 4 Potential 5 Kinetic-En. 6 Total-Energy 7 Temperature 8 Pressure-(bar) 9 Box-X 10 Box-Y 11 Box-Z 12 Volume 13 Density-(SI)14 pV 15 Vir-XX 16 Vir-XY 17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ 21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX-(bar) 25 Pres-XY-(bar) 26 Pres-XZ-(bar) 27 Pres-YX-(bar) 28 Pres-YY-(bar) 29 Pres-YZ-(bar) 30 Pres-ZX-(bar) 31 Pres-ZY-(bar) 32 Pres-ZZ-(bar) 33 #Surf*SurfTen 34 Mu-X35 Mu-Y36 Mu-Z 37 T-SOL 38 Lamb-SOL 8 0 Last energy frame read 2 time 4000.000 Statistics over 201 steps [ 0. thru 4000.0002 ps ], 1 data sets All averages are exact over 201 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Pressure (bar) 0.868069194.562194.557 0.00116891 4.67564 Thank you, Lum -- 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] Genbox
Hello all, How long does it usually take genbox to run? Thanks, Lum -- 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:How to check for bad contacts.
Hello Dr. Warren, Thank you for the useful information. I did use vmd to view my molecule, but in a system of 2000 molecules, it is quite difficult to locate atom 2065 (an O atom) which is actually the offending atom. I have described the way I did the work below. I used a random generator software for starting coordinates. How do you reassign a randomly generated coordinate? The way I generated my initial coordinates for 2000 water is by first drawing one molecule in ghemical, exported as a .pdb file, then used the command below to add 2000 molecules of water to a box of dimensions 40 A using a software for random coordinate generation called Packmol: tolerance 2.0 output waters2000.pdb filetype pdb structure water.pdb number 2000 inside cube 0. 0. 0. 40. end structure I then used editconf to change from .pdb to .gro since charmm27, which is the forcefield I use, is not among the force fields displayed when I use the pdb2gmx command. editconf -f waters2000.pdb -o waters2000.gro This editconf command reduces the previously defined box dimensions to zero. So, I use this command to re-define the box dimensions and I don't know if it is correct: editconf -bt cubic -box 4.0 -f waters2000.gro -o waters2000d.gro I then minimize the system via grompp and further minimize the system via mdrun, then I get the error message that my system cannot be settled. grompp -f waters_min.mdp -c waters2000d.gro -p water.top -o wmin_.tpr mdrun -nice 0 -v -s wmin_.tpr -o wmin.trr -c waters2000d.gro -e wmin_ener.edr Output of minimization: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 500 Step=0, Dmax= 1.0e-02 nm, Epot= 4.93923e+14 Fmax= 1.81064e+17, atom= 2035 Step=1, Dmax= 1.0e-02 nm, Epot= 3.85283e+11 Fmax= 8.96443e+13, atom= 2035 Step=2, Dmax= 1.2e-02 nm, Epot= 2.83666e+09 Fmax= 4.79912e+11, atom= 2035 Step=3, Dmax= 1.4e-02 nm, Epot= 5.92577e+07 Fmax= 7.02630e+09, atom= 2035 Step=4, Dmax= 1.7e-02 nm, Epot= 5.71720e+06 Fmax= 2.14598e+08, atom= 793 Step=5, Dmax= 2.1e-02 nm, Epot= 1.46839e+06 Fmax= 2.37662e+07, atom= 4936 Step=6, Dmax= 2.5e-02 nm, Epot= 6.41000e+05 Fmax= 2.52111e+06, atom= 3232 Step=7, Dmax= 3.0e-02 nm, Epot= 2.73384e+05 Fmax= 5.96696e+05, atom= 3688 Step=8, Dmax= 3.6e-02 nm, Epot= 1.64413e+05 Fmax= 1.55972e+05, atom= 2686 Step=9, Dmax= 4.3e-02 nm, Epot= 1.09639e+05 Fmax= 3.25690e+04, atom= 2389 Step= 10, Dmax= 5.2e-02 nm, Epot= 5.32635e+04 Fmax= 2.60651e+04, atom= 2065 t = 0.022 ps: Water molecule starting at atom 2065 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Thank you, Lum -- 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] How to check for bad contacts
Hello, How do you check for bad contacts in a system that cannot be minimized? Thanks, Lum -- 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] Calculating density of a particular run segment
Hello all, I have tried this command line to find the density of a system at particular time interval: g_density -f traj.xtc -s topol.tpr -b 1228 -e 1328 -o density.xvg, but I keep having the result to the full mdrun. The plot of the density vs box dimension is also obtained via xmgrace. I need to plot this density in terms of time. Is it possible to do so? Also, I need help with help with adjusting the above command line so that I can find the density of only one segment of the run. Thanks, Lum -- 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] Problem with system minimization
Hello all, I am minimizing a system of 2000 water molecules again but I have several error messages. Is my timestep too large indeed? The error message also mentions segmentation fault. I have only 6000 atoms in my system but the output shows atom 7783 and 8879. I'm not sure what's going on. My pdb file is shown below and the output of the minimization is written after the output. Please, help me locate the problem. ; VARIOUS PREPROCESSING OPTIONS title= NPT simulation of water cpp = /lib/cpp include = -I../top define = ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 5000 simulation_part = 1 init_step= 0 comm-mode= Linear nstcomm = 1 ; LANGEVIN DYNAMICS bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS emtol= 1000 emstep = 0.01 ; OUTPUT CONTROL OPTIONS nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 100 xtc-precision= 1000 xtc-grps = SOL energygrps = SOL ; ; PARAMETERS FOR NEIGHBORSEARCHING nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 0.9 ; ELECTROSTATICS AND VDW OPTIONS coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes t = 4.066 ps: Water molecule starting at atom 1993 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 2034, Dmax= 3.4e-02 nm, Epot= 1.48017e+09 Fmax= 1.08293e+08, atom= 7783 Step= 2035, Dmax= 4.0e-02 nm, Epot= 1.46516e+09 Fmax= 1.83787e+09, atom= 1993 Step= 2037, Dmax= 2.4e-02 nm, Epot= 1.44351e+09 Fmax= 2.34469e+08, atom= 1993 Step= 2038, Dmax= 2.9e-02 nm, Epot= 1.42904e+09 Fmax= 4.29069e+08, atom= 1993 Step= 2039, Dmax= 3.5e-02 nm, Epot= 1.41457e+09 Fmax= 2.10114e+08, atom= 1993 Step= 2040, Dmax= 4.2e-02 nm, Epot= 1.39993e+09 Fmax= 3.01888e+08, atom= 1993 Step= 2042, Dmax= 2.5e-02 nm, Epot= 1.38636e+09 Fmax= 2.28092e+08, atom= 4549 Step= 2043, Dmax= 3.0e-02 nm, Epot= 1.37259e+09 Fmax= 1.40258e+08, atom= 4549 Step= 2044, Dmax= 3.6e-02 nm, Epot= 1.35660e+09 Fmax= 4.77136e+08, atom= 4549 Step= 2045, Dmax= 4.3e-02 nm, Epot= 1.34145e+09 Fmax= 1.32867e+08, atom= 4549 Step= 2047, Dmax= 2.6e-02 nm, Epot= 1.32970e+09 Fmax= 3.61866e+08, atom= 3097 Step= 2048, Dmax= 3.1e-02 nm, Epot= 1.31958e+09 Fmax= 3.14277e+08, atom= 3097 Step= 2049, Dmax= 3.7e-02 nm, Epot= 1.31567e+09 Fmax= 9.12713e+08, atom= 3964 Step= 2050, Dmax= 4.5e-02 nm, Epot= 1.30841e+09 Fmax= 6.21777e+08, atom= 3964 Step= 2051, Dmax= 5.4e-02 nm, Epot= 1.30480e+09 Fmax= 5.82421e+08, atom= 3637 t = 4.104 ps: Water molecule starting at atom 3637 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 2052, Dmax= 6.5e-02 nm, Epot= 1.29311e+09 Fmax= 4.72304e+08, atom= 3079 t = 4.106 ps: Water molecule starting at atom 3079 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 2054, Dmax= 3.9e-02 nm, Epot= 1.27930e+09 Fmax= 1.93571e+08, atom= 8879 Step= 2056, Dmax= 2.3e-02 nm, Epot= 1.26788e+09 Fmax= 3.64079e+08, atom= 1411 Step= 2057, Dmax= 2.8e-02 nm, Epot= 1.25869e+09 Fmax= 2.08411e+08, atom= 5857 Step= 2058, Dmax= 3.4e-02 nm, Epot= 1.24544e+09 Fmax= 1.25967e+08, atom= 5857 Step= 2060, Dmax= 2.0e-02 nm, Epot= 1.23279e+09 Fmax= 1.91600e+08, atom= 1411 Step= 2061, Dmax= 2.4e-02 nm, Epot= 1.22254e+09 Fmax= 1.33277e+08, atom= 88 Step= 2062, Dmax= 2.9e-02 nm, Epot= 1.20834e+09 Fmax= 1.80612e+08, atom= 1411 Step= 2063, Dmax= 3.5e-02 nm, Epot= 1.20371e+09 Fmax= 4.86526e+08, atom= 1411 Step= 2064, Dmax= 4.2e-02 nm, Epot= 1.20033e+09 Fmax= 8.14034e+08, atom= 5857 Step= 2065, Dmax= 5.0e-02 nm, Epot= 1.18726e+09 Fmax= 3.57392e+08, atom= 2851 Step= 2067, Dmax= 3.0e-02 nm, Epot= 1.18000e+09 Fmax= 3.11047e+08, atom= 2851 Step= 2068, Dmax= 3.6e-02 nm, Epot= 1.17184e+09 Fmax= 3.86104e+08, atom= 4048 Step= 2069, Dmax= 4.3e-02 nm, Epot= 1.16512e+09 Fmax= 3.59701e+08, atom= 4162 Step= 2070, Dmax= 5.2e-02 nm, Epo
[gmx-users] Determination of heat capacity of water at constant pressure
Dear All, Can someone give me an explanation of how to calculate the heat capacity of water at constant pressure after completion of the mdrun? Thank you, Lum ___ 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 output on terminal
Hello everyone, I had written earlier today about my concern involving grompp. I am trying to minimize the energy of a pure water system using grompp: grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr and part of the output on the terminal is as follows: Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top /aminoacids.dat There are: 2000 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing The problem is I am not specifying any aminoacid file and I am not doing a parallel run, but the aminoacid.dat file is being opened and the program assumes that I am doing a parallel run. Is this the way it should be, and will this affect my run results? Please help me out and be patient with me as I am still learning gromacs. Thanks, Lum ___ 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] Opening aminoacids.dat file during grommp
Hello all, I am running grommp which kind of goes "successfully" but I am a little concerned about the fact that one of the messages in the terminal says "opening aminoacids.dat file" and in another message says "OTHER: 2000 residues found." I guess this 2000 is refering to the 2000 water molecules in my system since I am using just pure water and the command line I am using is: grompp -f waters.mdp -c waters2000_b.gro -p waters2000.top -o watersinput.tpr I did not specify an amino acid file and I am not sure where that statement "opening aminoacids.dat file" is coming from. Will this affect my run? Please help me out. Lum ___ 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] Error message: Cut-off length is longer than half the shortest box vector
Hello everyone, Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very useful inputs to my quest for generating a .gro file from a .pdb file. I am now trying to minimize the energy of the system so I can do an mdrun but I keep having the error message: the cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I have changed the values of rlist, rvdw and rcoulomb, and even the box size several times but I still keep having this message. Please, I need help to figure out what to do to fix this problem. The command line I am using is:grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr Also, is there a way to convert atom types from one format to another? I also have the following warnings: "Warning: atom name 1 in water.top and waters_b.gro does not match (OW - O) Warning: atom name 2 in water.top and waters_b.gro does not match (HW1 - H) Warning: atom name 3 in water.top and waters_b.gro does not match (HW2 - H) atom names from water.top will be used atom names from waters_b.gro will be ignored." I had drawn my molecule in ghemical and exported as a pdb file and so the atom types O and H were automatically generated. Thank you, Lum ___ 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] Generating a .gro file from .pdb file
Hello everyone, Thanks to Justin Lemkul and Thomas Schlesier for replying to my question in vol. 65 issues 96 and 98. I am trying to convert a pdb file to a gro file using pdb2gmx -f waters.pdb -o waters.gro and I get the message: Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges I don't want to use any of these force fields. I want to use the charmm27 one. How do I select that? Do I need to modify the code? If so, where do I find it? Also, I read in a Spidertoxin tutorial that editconf can be used to convert a .pdb file to a .gro file. I tried this but error message says: "No velocities found." I know that pdb files generally do not have velocities and these velocities can be generated by setting genvel=yes in the mdp file. How can a .pdb file contain initial velocities? Thank you, Lum ___ 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
