Re: RE: [gmx-users] viscosity calculation using g_energy (3.3.3)
Dear Berk, Thanks for the reply. I have read through your paper. I have still some doubts. When used tcafś I got files called tcaf_all.xvg tcaf_fit.xvg tcaf.xvg visc_k.xvg ( all default names). I think, the file which I should use for fitting, using the formula eta(k) = eta (0) (1-ak²) + O(k^4) the viscoty ( viscosity - k vector plot) is visc_k.xvg. Am I right? IF yes, what all other files ( tcf_all.xvg, tcaf_fit.xvg and tcaf.xvg) do? expecting your reply, Jestin On Fri, 13 Mar 2009 Berk Hess wrote : > >Hi, > >I don't understand what you are actually doing now. >You seem to be mixing multiple methods. > >First off all, I would use NPT for all methods, except the one that uses the >pressure fluctuation. >The pressure will have a large effect on the viscosity and if you run NVT you >need to have >exactly the right volume. > >If you use the cosine acceleration method, the 1/viscosity is printed in the >energy file, >g_energy will plot it for you. > >g_tcaf is only for use with an equilibrium simulation. >If you read the paper, you will have seen an expression to extrapolate the k=0. > >Berk > >Date: Fri, 13 Mar 2009 07:33:30 + > From: jesb...@rediffmail.com >To: gmx-users@gromacs.org >Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3) >CC: > > > Dear Berk and David, > > > > Thank you very much for your > appropriate and informative replies. I tried another method (traverse > current method) to calculate the shear viscosity ( a non equilibrium method, > which has been described in Berkś paper : Journal of Chemical Physics, > 116, page 209 ( Determining the shear viscosity of model liquids from > molecular dynamics simulations)), > > > >I used the g_tcaf utility (ie g_tcaf -f traj1.trr > -s binary.tpr -oc test.xvg) . As suggested by David, I increased the system > size ( from 500 to 2048 TIP4P molecules). I ran in NVT ensemble which allows > the pressure to fluctuate. > >Apart from that I added following options to my mdp file, where accelaration >of 1A/ps² was given to the system. > > > >;NON EQUILIBRIUM STUFF > >acc_grps = system > >accelerate= 0.1 0.0 0.0 > >cos_acceleration = 0.1 > > > > > > > >Moreover, I saved the trajectory in every 1ps ( so total 500 frames for a >500ps simulation) > > > >then, > > > >I got the following output: > >k 1.593 tau 1.000 eta 0.09835 10^-3 kg/(m s) > >k 1.593 tau 1.000 eta 0.09835 10^-3 kg/(m s) > >k 1.593 tau 1.000 eta 0.09835 10^-3 kg/(m s) > >k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) > >k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) > >k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) > >k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) > >k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) > >k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) > >k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) > >k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) > >k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) > >k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) > >k 3.185 tau 1.000 eta 0.02459 10^-3 kg/(m s) > >k 3.185 tau 1.000 eta 0.02459 10^-3 kg/(m s) > >k 3.185 tau 1.000 eta 0.02459 10^-3 kg/(m s) > > > >- > > > >Which shows a strong k dependence over the property: shorter k, better the >viscosity, as pointed out in the paper. However, the value obtained is around >0.01 times less than the experimental value (1pa-second). Adding to that, the >results obtained by this method seems to be very convincing unlike the >g_energy that shows a great divergence!! > > > >So the situation is getting better now. Now, I would like to know whether this >can be improved if I save the trajectories more frequently ( 500 fs) and run >for longer, say 2ns or change value of accelaration . > > > >Any thoughts ? > > > > > >regards, > >Jes. > > > > > >On Thu, 12 Mar 2009 Berk Hess wrote : > > > > > >Hi, > > > > > >This is a very inefficient method for determining the viscosity. > > >Also you need really perfect pressure fluctuations: NVT, shifted potentials, > > >probably even double precision. > > >There was a mail about this recently. > > >There are better methods, have a look at: > > >http://dx.doi.org/10.1063/1.1421362 > > > > > >Berk > > > > > >Date: Thu, 12 Mar 2009 07:39:52 + > > > From: jesb...@rediffmail.com > > >To: gmx-users@gromacs.org > > >Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3) > > >CC: > > > > > > > > >David, > > > > > > > > > > > >Thanks for the quick reply. > > > > > > > > > > > >Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg > > > > > > > > > > > >The output file created includes three columns. > > > > > > > > > > > >1. time ( ps) 2. shear viscosit
Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
Dear Berk and David, Thank you very much for your appropriate and informative replies. I tried another method (traverse current method) to calculate the shear viscosity ( a non equilibrium method, which has been described in Berkś paper : Journal of Chemical Physics, 116, page 209 ( Determining the shear viscosity of model liquids from molecular dynamics simulations)), I used the g_tcaf utility (ie g_tcaf -f traj1.trr -s binary.tpr -oc test.xvg) . As suggested by David, I increased the system size ( from 500 to 2048 TIP4P molecules). I ran in NVT ensemble which allows the pressure to fluctuate. Apart from that I added following options to my mdp file, where accelaration of 1A/ps² was given to the system. ;NON EQUILIBRIUM STUFF acc_grps = system accelerate= 0.1 0.0 0.0 cos_acceleration = 0.1 Moreover, I saved the trajectory in every 1ps ( so total 500 frames for a 500ps simulation) then, I got the following output: k 1.593 tau 1.000 eta 0.09835 10^-3 kg/(m s) k 1.593 tau 1.000 eta 0.09835 10^-3 kg/(m s) k 1.593 tau 1.000 eta 0.09835 10^-3 kg/(m s) k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) k 2.252 tau 1.000 eta 0.04917 10^-3 kg/(m s) k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) k 2.759 tau 1.000 eta 0.03278 10^-3 kg/(m s) k 3.185 tau 1.000 eta 0.02459 10^-3 kg/(m s) k 3.185 tau 1.000 eta 0.02459 10^-3 kg/(m s) k 3.185 tau 1.000 eta 0.02459 10^-3 kg/(m s) - Which shows a strong k dependence over the property: shorter k, better the viscosity, as pointed out in the paper. However, the value obtained is around 0.01 times less than the experimental value (1pa-second). Adding to that, the results obtained by this method seems to be very convincing unlike the g_energy that shows a great divergence!! So the situation is getting better now. Now, I would like to know whether this can be improved if I save the trajectories more frequently ( 500 fs) and run for longer, say 2ns or change value of accelaration . Any thoughts ? regards, Jes. On Thu, 12 Mar 2009 Berk Hess wrote : > >Hi, > >This is a very inefficient method for determining the viscosity. >Also you need really perfect pressure fluctuations: NVT, shifted potentials, >probably even double precision. >There was a mail about this recently. >There are better methods, have a look at: >http://dx.doi.org/10.1063/1.1421362 > >Berk > >Date: Thu, 12 Mar 2009 07:39:52 + > From: jesb...@rediffmail.com >To: gmx-users@gromacs.org >Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3) >CC: > > >David, > > > >Thanks for the quick reply. > > > >Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg > > > >The output file created includes three columns. > > > >1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity. > > > >It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second). > > > >The bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( >Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two >order of magnitude. I wonder whether I have done anything wrong while >specifying the frequency of saving energy file. > > > >I have saved the energy file in every 2ps. Isn´t that enough for a simple >system like water? OR should I have to save trajectories in every 5fs as >suggested by one in a previous post. > > > >I post the first 20 lines of the output file. > > > >--- > > > ># This file was created Thu Mar 12 16:20:09 2009 > ># by the following command: > ># g_energy -f water.edr -vis test.xvg > ># > ># g_energy is part of G R O M A C S: > ># > ># GROup of MAchos and Cynical Suckers > ># > >@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" > >1.99203 9.6633 96.3893 > >3.98406 11.1625 98.1365 > > 5.9761 12.6631 99.838 > >7.96813 13.4652 101.366 > >9.96016 13.7012 100.249 > >- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please s
Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
David, Thanks for the quick reply. Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg The output file created includes three columns. 1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity. It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second). The bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two order of magnitude. I wonder whether I have done anything wrong while specifying the frequency of saving energy file. I have saved the energy file in every 2ps. Isn´t that enough for a simple system like water? OR should I have to save trajectories in every 5fs as suggested by one in a previous post. I post the first 20 lines of the output file. --- # This file was created Thu Mar 12 16:20:09 2009 # by the following command: # g_energy -f water.edr -vis test.xvg # # g_energy is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @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" 1.99203 9.6633 96.3893 3.98406 11.1625 98.1365 5.9761 12.6631 99.838 7.96813 13.4652 101.366 9.96016 13.7012 100.249 - regards, Jes On Thu, 12 Mar 2009 David van der Spoel wrote : >JMandumpal wrote: >>Dear GROMACS users, >> >> As explained in the manual ( page 139, section >> 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using >> g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit >> written on the Y axis of the corresponding xvg file is (kJ mol\S-1\N). I >> think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. >> Then why is this discrepancy.? Or did I make any mistake? >> >Mu is the dipole (in Debye). The units of these things are incorrect for >everything that is not an energy. This will be fixed in the next gmx version. >g_energy -h tells you what to do: > >g_energy -f ener -vis viscosity > >> >>--I give the command on the prompt: >> >>g-energy -f ener.edr - o viscosity.xvg ; >>then chose option 40 ( Mu-X). >> >>system details: >>** >>My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at >>150K, the ensemble is NPT. The version I am using is 3.3.3 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] viscosity calculation using g_energy (3.3.3)
Dear GROMACS users, As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit written on the Y axis of the corresponding xvg file is (kJ mol\S-1\N). I think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. Then why is this discrepancy.? Or did I make any mistake? --I give the command on the prompt: g-energy -f ener.edr - o viscosity.xvg ; then chose option 40 ( Mu-X). system details: ** My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 150K, the ensemble is NPT. The version I am using is 3.3.3 regards, Jes___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users]Simulated annealing
Dear Xavier and Jochen, Thank you for the suggestions: it works well now. Jes. On Mon, 27 Oct 2008 Xavier Periole wrote : >On 27 Oct 2008 06:36:09 - > "JMandumpal" <[EMAIL PROTECTED]> wrote: >> Dear GROMACS users, >> >>I have got a problem while running a simulated anealing simulations, using >>GROMACS 3.3.3 version, of pure water: >> >>the task: >> >>I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps >>time ( fast cooling). For that I used the following script: >> >>title= Water annealing simulation >>cpp = /usr/bin/cpp >>; RUN CONTROL PARAMETERS >>integrator = md >>; Start time and timestep in ps >>dt = 0.001; 1fs >>nsteps = 10 ; 1ps >>; For exact run continuation or redoing part of a run >>init_step = 0 >>; number of steps for center of mass motion removal >>nstcomm = 1 >>; group(s) for center of mass motion removal >>comm-grps= SOL >>; OUTPUT CONTROL OPTIONS >>; Output frequency for coords (x), velocities (v) and forces (f) >>nstxout = 1 ; 10ps >>nstvout = 1 ; 10ps >>nstfout = 0 >>; Checkpointing helps you continue after crashes >>nstcheckpoint= 100 >>; Output frequency for energies to log file and energy file >>nstlog = 0 >>nstenergy= 1000 ; 1ps >>; Output frequency and precision for xtc file >>;nstxtcout= 0 >>;xtc-precision= 1000 >>; select multiple groups. By default all atoms will be written. >>; NEIGHBORSEARCHING PARAMETERS >>nstlist = 10 >>; ns algorithm (simple or grid) >>ns_type = grid >>; Periodic boundary conditions: >>pbc = xyz >>; nblist cut-off >>rlist= 1.0 >>; OPTIONS FOR ELECTROSTATICS AND VDW >>; Method for doing electrostatics >>coulombtype = pme >>rcoulomb = 1.0 >>ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol >>optimize_fft = yes >>; Relative dielectric constant for the medium >>epsilon_r= 1 ; for water >>; Method for doing Van der Waals >>vdw-type = cut-off >>rvdw = 1.0 >>; Spacing for the PME/PPPM FFT grid >>fourierspacing = 0.12 ; check for the range 0.1 to 0.15 >>; EWALD/PME/PPPM parameters >>pme_order= 4 >>ewald_geometry = 3d >>epsilon_surface = 0 >>; OPTIONS FOR WEAK COUPLING ALGORITHMS >>; OPTIONS FOR WEAK COUPLING ALGORITHMS >in what follows you have commented out the temperature coupling details. >I have never used SA but this for sure will not help the program controling >the temperature! Put these back on should help! :)) >>; Temperature coupling >>;Tcoupl = berendsen >>; Groups to couple separately >>;tc-grps = system >>; Time constant (ps) and reference temperature (K) >>;tau-t = 0.1 >>;ref-t= 360 >>; simulated anealing >>annealing= single >>annealing_npoints= 2 >>annealing_time = 0 0 >>annealing_temp = 360 0 >>; GENERATE VELOCITIES FOR STARTUP RUN >>gen_vel = yes >>gen-temp = 360 >>gen-seed = 173529 >>; OPTIONS FOR BONDS >>constraints = all-bonds >>constraint_algorithm = shake >>shake_tol= 0.0001 >>morse= no >> >> >> --- >> >>Problem: >> >>Having done the simulations, the output shows ( ener.edr , Temperature) a >>high temperature value around 850K. Clearly I did something wrong in my >>parameter file. >>--- >>the temperature extracted after the simulations >>--- >>s0 legend "Temperature" >>0.00 376.058044 >>1.00 864.033020 >>2.00 873.607605 >>3.00 851.308838 >>4.00 847.223877 >
[gmx-users]Simulated annealing
Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title= Water annealing simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps dt = 0.001; 1fs nsteps = 10 ; 1ps ; For exact run continuation or redoing part of a run init_step = 0 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 ; 10ps nstvout = 1 ; 10ps nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 ; Output frequency for energies to log file and energy file nstlog = 0 nstenergy= 1000 ; 1ps ; Output frequency and precision for xtc file ;nstxtcout= 0 ;xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; check for the range 0.1 to 0.15 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling ;Tcoupl = berendsen ; Groups to couple separately ;tc-grps = system ; Time constant (ps) and reference temperature (K) ;tau-t = 0.1 ;ref-t= 360 ; simulated anealing annealing= single annealing_npoints= 2 annealing_time = 0 0 annealing_temp = 360 0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen-temp = 360 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no --- Problem: Having done the simulations, the output shows ( ener.edr , Temperature) a high temperature value around 850K. Clearly I did something wrong in my parameter file. --- the temperature extracted after the simulations --- s0 legend "Temperature" 0.00 376.058044 1.00 864.033020 2.00 873.607605 3.00 851.308838 4.00 847.223877 5.00 860.511841 6.00 813.547241 7.00 845.261658 8.00 872.090027 9.00 852.079468 10.00 849.152466 11.01 850.055237 12.01 834.468323 13.01 861.107300 14.01 828.380493 15.01 850.166809 16.00 850.382019 17.00 847.214478 18.00 851.201538 19.00 857.533691 20.00 849.760071 21.02 864.907715 22.02 837.307495 23.02 827.407593 24.02 841.464111 25.02 863.330688 26.02 841.096069 27.02 856.469910 28.02 854.449768 29.02 845.534973 30.02 853.421448 31.02 825.198059 32.00 857.317566 33.00 823.510925 34.00 858.875122 35.00 880.710266 36.00 853.692749 37.00 847.079468 38.00 851.004822 39.00 858.75 40.00 872.787048 41.04 843.033813 42.04 874.984009 43.04 845.272583 44.04 822.993713 45.04 863.116455 46.04 865.640198 47.04 873.489563 48.04 849.170776 49.04 861.631958 50.0
[gmx-users] cooling the system "NVT" ensemble
Dear GROMACS users, A method to locate glass transtion temperature of liquids is reported by Stanley et al, PRL 2004, 93, pp 047801: system is cooled initially and then is heated , in the range 0K-400K, in a "modified" NVT ensemble. (Total energies of the system with respect to temp. is plotted, a kink in the plot is refered to the glass transition) In a standard NVT simulation, To is constant. In this method, the Berendsen thermostat is used but, at everytime step, the bath temperature To is updated such that To(t)= To(t=0) + deltaT, with deltaT= cooling/heating * timestep. This is done at every time step before rescaling the velocities. Now, I would like to know how can I 'impliment' this in a GROMACS version; I mean where should I modify the code? Or is there any other way to achieve this without modifying the code? Is it /usr/local/gromacs/src/mdlib/tgroup.c ? Thanks for your help, Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PBS script for gromacs Gromacs
Dear Manoj, Here is the script, for running parallel, which I am using. You may need to change it according to your machine-specifications. --script for GROMACS 3.3.3- #!/bin/bash #PBS -l vmem=8gb #PBS -l jobfs=10GB #PBS -l ncpus=4 #PBS -l software=gromacs #PBS -l other=mpi #PBS -wd #PBS -q express module load intel-cc/10.0.023 module load intel-fc/10.0.023 module load gromacs/3.3.3 grompp -np $PBS_NCPUS -f em.mdp -p topol.top -c conf.gro -o binary.tpr mpirun mdrun -s binary.tpr -o traj1.trr -c out1.gro -g sim.log On Mon, 21 Jul 2008 Manoj Kumar Singh wrote : >Hi, > >I am new with Gromacs and I don't know how to submit job on cluster. I am >looking for a PBS script. I am using cluster made of Intel Xeon CPU E5345. >The mpi Gromacs has already been installed. > >I will be very thankful for any response. > >Manoj ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] make_ndx problem
I think, after creating an index file, you can edit it manually clubbing both Phosphorius and Oxygen atoms together ( considering as a single group). Then specify this group while doing analysis. On Wed, 16 Jul 2008 minnale wrote : > Thanks for the reply, may be this is trivial question to you >That I know that how to select phosrous atom alone of POPC. >Normally people are using only phosphrous atom or PO4 group ? for density >calculation ,etc analysis. In one article I found that they have done density >analysis for PO4 group. >Could you please tell me which one use it for analysis if PO4 how select by >using make_ndx? >Thanks alot in advance. > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] (no subject)
I think, setting tc groups = system will solve this issue. On Thu, 17 Jul 2008 Justin A.Lemkul wrote : >For warnings/errors, etc. please check the archive and wiki before posting. I >just responded to a similar issue a few days ago: > >http://www.gromacs.org/pipermail/gmx-users/2008-June/034786.html > >-Justin > >[EMAIL PROTECTED] wrote: >>Hi all >>I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2. >>so check i tried to to do speptide tutorial in >>/usr/local/gromacs/share/gromacs/tutor/speptide >> >>But when i m running grompp for position restraint with the command >>grompp -f pr -o pr -c after_em -r after_em -p speptide >> >>i get the following warning >> >> WARNING 1 [file aminoacids.dat, line 1]: >> T-Coupling group Protein has fewer than 10% of the atoms (191 out of >> 2741) >> Maybe you want to try Protein and Non-Protein instead? >> >>I tried to change SOL with non protein but getting the same warning. is it >>ok to go further with this warning >> >>When i did grompp for full MD with the command >> >>grompp -v -f full -o full -c after_pr -p speptide >> >>again i m getting the same warning >> >>WARNING 1 [file aminoacids.dat, line 1]: >> T-Coupling group Protein has fewer than 10% of the atoms (191 out of >> 2741) >> Maybe you want to try Protein and Non-Protein instead? >> >> >>I tried to change SOL with non protein but getting the same warning. >> >>I don't know what to do now and how can i overcome this, if anyone could >>help me. >> >>Thanks >> >>ALKA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to define NVE ensemble in gromacs
Disable Temperature and Pressure coupling parameters in your script and variables related to them as well. Tcoupl = no Pcoupl = no On Wed, 09 Jul 2008 beibei wrote : >Hi, all >How to define NVE ensemble in mdp file? thanks. > > beibei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Meaning of CT, C_2, C_3 in ffoplsaabon.itp
Dear Gayen, It stands for different atom types of the same element. For instance, in all atom OPLS parameter model for acetone, following atom types are being used. CT, 0_2, C_2 and HC for methyl carbons, keto oxygen, carbonyl carbon and methyl hydrogens respectively. Indeed, CT( for methyl Carbon) and C_2 (for keto carbon) have to be specific, especially when bond angle, length and dihedral ( in the parameter file ) are mentioned. Hope this helps. On Mon, 23 Jun 2008 Mark Abraham wrote : >ANINDITA GAYEN wrote: >> >>--- On Mon, 23/6/08, ANINDITA GAYEN <[EMAIL PROTECTED]> wrote: >> >>> From: ANINDITA GAYEN <[EMAIL PROTECTED]> >>>Subject: To: gmx-users@gromacs.org >>>Date: Monday, 23 June, 2008, 11:47 AM >>>Hello Al, >>> >>> >>>Can someone tell me what is the meaning of CT, CT_2, C_3, >>>C_2 etc atomtypes defined in the ffoplsaabon.itp? I have >>>not found it in the manual. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Crashing NPT run, 1.5 ns
Dear list, When I changed the time step to 1fs, the simulations were successful. What could be wrong with timestep 2.0 fs. I am using GROMAXS version 3.3.3 regards Jes On Wed, 28 May 2008 JMandumpal wrote : >Dear list, > >I was running AA acetone with tip4p water for calculating average density : >NPT for 1.5 ns, but, after 600 ps the simulation crashes . I came to know from >older posts, this may result with an inappropriate value of P-couple. I >increased the value from 0.4, which was using before, to 5.0, still the >simulation crashes. I paste the error message, the input file for the >simulation and the parameter file for acetone. Could you please point out >where I did make mistake. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] acetone parameter
Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE -- [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_0691 ACETCAA 10.000 15.0350 2 opls_2801 ACETC_2 10.470 12.0110 3 opls_0691 ACETCAD 10.000 15.0350 4 opls_2811 ACETO_2 1 -0.470 15.9994 --- But on the other hand, when I checked the literature, JPC 94, 1990, p.1683, I found out, the parameters are given in the following manner, TABLE TWO : TABLE TWO atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O -0.424 2.960 0.210 ** For keeping total charge in the system to zero, I used the opls_069 for methyl group (zero charge), in my input file, compared to what has been published. I would like to know whether the parameters (charge) I chose is right, else which atom type I must use for methyl group. thanking in advance, Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Epsilon in ffoplsaanb.itp
Dear list, The OPLS parameter for S in DMSO is zigma 0.395 and epsilon 3.56 A ( JACS 1996, 118, 4175-4180) But in the ffoplsaanb.itp (/gromacs/3.3.2-dp/share/gromacs/top) it is given as below: - name bond_typemasscharge ptype sigma epsilon opls_124 S 16 32.06000 0.139 A3.56000e-01 1.65268e+00 -- (a change in value of epsilon; 1.65268 instead of 3.56 A) Is this a mistake? thanks in advance, Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Unit of diffusion coefficient
Dear list, Since the unit is not printed in the .xvg file generated by the module g_msd in GROMACS 3.3.2 version , I would like to know the unit of diffusion coefficient calculated. Is it in cm^2/ sec or m^2/sec? regards, jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] NVT and NVE
Hi Markus, Thanks for the reply. It worked fine. Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] NVT and NVE
Hi Markus, It means that I should change cutoff to the Shift, right (manual 7.3.10) jes On Sat, 05 Apr 2008 Markus Miettinen wrote : >Hi Jes, > > > to me it seems that you have rlist = rvdw: > >>nstlist = 10 >>rlist= 1.0 >>rvdw = 1.0 > > > This will lead to a loss of energy, because between list updates > two particles originally at distance, say, 1.01 from each other > can easily move within rvdw from each other, but they will not > "see" each other until the lists are updated again. > > In other words, you have particles moving within the attractive > LJ-potential region without giving them the speed-up that the > attractive potential should provide. This mistake equals loss of > energy, and becomes apparent in NVE. In NVT the thermostat > (artificially!) fixes the energy loss. > > The correct way is to set rlist > rvdw. > > >Cheers, >markus. > >-- >Halli delendum est. > >On Apr 3, 2008, at 13:00 , [EMAIL PROTECTED] wrote: > >>Date: 3 Apr 2008 08:12:40 - >> From: "JMandumpal" <[EMAIL PROTECTED]> >>Subject: Re: Re: [gmx-users] NVT and NVE >>To: "Discussion list for GROMACS users" >>Message-ID: <[EMAIL PROTECTED]> >>Content-Type: text/plain; charset="iso-8859-1" >> >>Dear David, >> >>I post the input file for the NVE run. >> >>I use SHAKE, Would it be better if I use LINCS? >> >>title= NVE >>cpp = /usr/bin/cpp >>; RUN CONTROL PARAMETERS >>integrator = md >>; Start time and timestep in ps >>tinit= 500 >>dt = 0.0015; >>nsteps = 36; 540 ps >>; For exact run continuation or redoing part of a run >>init_step= 0 >>; number of steps for center of mass motion removal >>nstcomm = 1 >>; group(s) for center of mass motion removal >>comm-grps= SOL >>; OUTPUT CONTROL OPTIONS >>; Output frequency for coords (x), velocities (v) and forces (f) >>nstxout = 0 >>nstvout = 0 >>nstfout = 0 >>; Checkpointing helps you continue after crashes >>nstcheckpoint= 1000 >>; Output frequency for energies to log file and energy file >>nstlog = 10 >>nstenergy= 1000 >>; Output frequency and precision for xtc file >>nstxtcout= 0 >>xtc-precision= 1000 >>; select multiple groups. By default all atoms will be written. >>; NEIGHBORSEARCHING PARAMETERS >>nstlist = 10 >>; ns algorithm (simple or grid) >>ns_type = grid >>; Periodic boundary conditions: >>pbc = xyz >>; nblist cut-off >>rlist= 1.0 >>; OPTIONS FOR ELECTROSTATICS AND VDW >>; Method for doing electrostatics >>coulombtype = pme >>rcoulomb = 1.0 >>ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff) =ewald_rtol >>optimize_fft = yes >>; Relative dielectric constant for the medium >>epsilon_r= 1 ; for water >>; Method for doing Van der Waals >>vdw-type = cut-off >>rvdw = 1.0 >>; Spacing for the PME/PPPM FFT grid >>fourierspacing = 0.12 ; >>; EWALD/PME/PPPM parameters >>pme_order= 4 >>ewald_geometry = 3d >>epsilon_surface = 0 >>; OPTIONS FOR WEAK COUPLING ALGORITHMS >>; Temperature coupling >>Tcoupl = no >>Pcoupl = no >>; GENERATE VELOCITIES FOR STARTUP RUN >>gen_vel = no >>gen-temp = 300 >>gen-seed = 173529 >>; OPTIONS FOR BONDS >>constraints = all-bonds >>constraint_algorithm = shake >>shake_tol= 0.0001 >>morse= no >> >> >>rgds, >>Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] NVT and NVE
Dear David, I post the input file for the NVE run. I use SHAKE, Would it be better if I use LINCS? title= NVE cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 500 dt = 0.0015; nsteps = 36; 540 ps ; For exact run continuation or redoing part of a run init_step= 0 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no Pcoupl = no ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no rgds, Jes On Fri, 28 Mar 2008 David van der Spoel wrote : >JMandumpal wrote: >>Dear list, >> >> These are the energy I obtained running 60ps NVE of 500 TIP5P water >> molecules- I still wonder why the energy has not been converged even having >> run for 160 ps in total (100 NVT + 60 NVE). >> >> >it is difficult to run NVE. >what constraint settings etc. do you use and what cutoffs. > >> 100.00 -15887.623027 >> 101.50 -15887.961065 >> 103.00 -15894.289055 >> 104.50 -15898.915859 >> 106.00 -15903.562196 >> 107.50 -15906.540627 >> 109.00 -15912.662455 >> 110.50 -15915.571468 >> 112.00 -15917.889520 >> 113.50 -15923.955612 >> 115.00 -15929.135491 >> 116.50 -15932.507824 >> 118.00 -15937.882055 >> 119.50 -15941.562218 >> 121.00 -15945.644608 >> 122.50 -15949.063632 >> 124.00 -15953.389791 >> 125.50 -15957.524802 >> 127.00 -15962.299775 >> 128.50 -15967.579640 >> 130.00 -15972.576889 >> 131.50 -15975.427574 >> 133.00 -15980.852975 >> 134.50 -15985.584201 >> 136.00 -15988.488715 >> 137.50 -15993.295989 >> 139.00 -15997.867767 >> 140.50 -16000.630051 >> 142.00 -16005.100451 >> 143.50 -16009.649201 >> 145.00 -16014.842764 >> 146.50 -16019.498233 >> 148.00 -16022.975477 >> 149.50 -16027.677441 >> 151.00 -16032.965475 >> 152.50 -16036.043976 >> 154.00 -16039.844112 >> 155.50 -16044.836132 >> 157.00 -16047.992186 >> 158.50 -16052.196926 >> 160.00 -16056.946593 >> >> >>--- >>I corrected these variables to: >>tinit= 100 >> >>init_step= 0 >> >>Where could be the problem, then? Or should I run for even longer? >> >>regards, >>Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] NVT and NVE
Dear list, These are the energy I obtained running 60ps NVE of 500 TIP5P water molecules- I still wonder why the energy has not been converged even having run for 160 ps in total (100 NVT + 60 NVE). 100.00 -15887.623027 101.50 -15887.961065 103.00 -15894.289055 104.50 -15898.915859 106.00 -15903.562196 107.50 -15906.540627 109.00 -15912.662455 110.50 -15915.571468 112.00 -15917.889520 113.50 -15923.955612 115.00 -15929.135491 116.50 -15932.507824 118.00 -15937.882055 119.50 -15941.562218 121.00 -15945.644608 122.50 -15949.063632 124.00 -15953.389791 125.50 -15957.524802 127.00 -15962.299775 128.50 -15967.579640 130.00 -15972.576889 131.50 -15975.427574 133.00 -15980.852975 134.50 -15985.584201 136.00 -15988.488715 137.50 -15993.295989 139.00 -15997.867767 140.50 -16000.630051 142.00 -16005.100451 143.50 -16009.649201 145.00 -16014.842764 146.50 -16019.498233 148.00 -16022.975477 149.50 -16027.677441 151.00 -16032.965475 152.50 -16036.043976 154.00 -16039.844112 155.50 -16044.836132 157.00 -16047.992186 158.50 -16052.196926 160.00 -16056.946593 --- I corrected these variables to: tinit= 100 init_step= 0 Where could be the problem, then? Or should I run for even longer? regards, Jes ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] NVT and NVE
Dear Mark, Thank you very much for the reply. Well I used the following job script: #!/bin/bash #PBS -l vmem=800MB #PBS -l ncpus=4 #PBS -l jobfs=10MB #PBS -l software=gromacs #PBS -l other=mpi #PBS -q express #PBS -wd module load gromacs/3.3.2 grompp_d -np $PBS_NCPUS -f mdout_NVE.mdp -p topol.top -c conf_100ps.gro -t pr.trr -o binary.tpr mpirun mdrun_mpi_d -s binary.tpr -o pr1.trr -c output_1.gro -g topol.log Note: pr.trr is the trajectory from 100ps NVT simulations, and conf_100ps.gro is the equilibrated box from the same. -- MY .mdp file, for running NVE simulation after a 100ps equilibration with NVT, is pasted here: title= Howdie cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.0015; nsteps = 4 ; For exact run continuation or redoing part of a run init_step= 11 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no ; Groups to couple separately tc-grps = SOL ; Time constant (ps) and reference temperature (K) tau-t= 0.1 ref-t= 300 ; Pressure coupling Pcoupl = no Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 0.5 compressibility = 4.5e-5 ref-p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no I suspect I made something wrong in these variables; Could anyone please correct it? tinit= 0 ; For exact run continuation or redoing part of a run init_step= 11 regards, Jestin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] NVT and NVE
Dear lists, Should I use this : tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr -time 100 -until 160 and then mpirun mdrun_mpi_d -s tpxout.tpr -o pr.trr -c output_1.gro -g topol.log If then, how do I change my paremeters, for example to remove temprature coupling parameters in order to run NVE. regards, Jestin On Fri, 28 Mar 2008 JMandumpal wrote : >Dear gromacs users, > > >I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the energy >conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs, but these NVE >simulations seem not to converge even after. Following is the command I used >for running 60ps NVE : >-- >grompp_d -np $PBS_NCPUS -f mdout_NVE.mdp -p topol.top -c conf_100.gro -o >binary.tpr > >- >conf_100.gro is the equilibrated box, from my 100ps NVT, which I used for the >NVE's. Is this the right way of doing it? or Am I miss something else in those >commands. >My system is 500 TIP5P box. > > >regards, >Jestin > >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] NVT and NVE
Dear gromacs users, I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the energy conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs, but these NVE simulations seem not to converge even after. Following is the command I used for running 60ps NVE : -- grompp_d -np $PBS_NCPUS -f mdout_NVE.mdp -p topol.top -c conf_100.gro -o binary.tpr mpirun mdrun_mpi_d -s binary.tpr -o pr.trr -c output_1.gro -g topol.log - conf_100.gro is the equilibrated box, from my 100ps NVT, which I used for the NVE's. Is this the right way of doing it? or Am I miss something else in those commands. My system is 500 TIP5P box. regards, Jestin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:writing xtc file from trr file
>Dear all, >While running a job, since there was space problem I could not write the xtc >files. Now when I do the analysis and use the trr file it reports the >time >values after every 5ps i.e. 2000, 2005, 2010 etc. However I wish to >write the >xtc file using trjconv such that the timestep is reported >after every >picosecond. >Is this possible or do I need to rerun the entire simulation again to >get the >xtc file? >Regards, >Priyanka. Well, How about trying this command: trjconv -f *.trr -o *.xtc regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: RE: [gmx-users] TIP5P and cg minimization
Rob, I wonder whether you have got the flexible water model, TIP5P. I want to run simulations using the flexible TIP5P water model. Well, how does the results from the MD be affected if I use rigid water models in place of a flexible one? regards Jestin On Thu, 06 Mar 2008 rob yang wrote : > >Thanks Mark for the pointer. > >The TIP5P.itp has [settles] only, whereas TIP4P.itp (as well as spc.itp, and >TIP3P) has parameters for flexible water [FLEXIBLE] as well as rigid >[settles]. This, by definition would restrict any systems using TIP5P to the >SHAKE algorithm. I am wondering: >1) are there other TIP5P.itp files that possibly include the FLEXIBLE >parameters (force constants for bonds and angles)? >2) for my present TIP5P.itp, is this going to impact the MD run? > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] step.pdb files during EM
Dear list, I ran EM (energy minimisation) of TIP5P water model using gromacs/3.3.2 version. My output says : Steepest Descents converged to Fmax < 100 in 427 steps. Moreover, my output.gro file looks ok after the run. But in the directory, there were some files (8), called step.pdb, generated. But, it is said, actually simulation crashed, that is why these files are being generated ( Thread 2004 January). But in my case, if the program was crashed, then why it ran till 427th step to finish EM to the desired accuracy. Furthermore, when I inspected the output file, I found the following similar messages on 8 occasions : "t = 0.023 ps: Water molecule starting at atom 356 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates". I constructed the water box using packmol program. If I want to avoid these error messages, What should I do? thanks in advance, Jestin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] non-zero total charge for water
Dear Gromacs users, I built .tpr file prior to energy minimisation of box of tip5p water molecule. I received the output like this: calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 2 bonded neighbours for SOL 258 NOTE: System has non-zero total charge: -2.58e-01 processing coordinates... double-checking input for internal consistency... Cleaning up constraints and constant bonded interactions with virtual sites renumbering atomtypes... converting bonded parameters... # SETTLE: 258 # VSITE3OUT: 516 Setting particle type to V for virtual sites initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs/3.3.2-dp/share/gromacs/top/aminoacids.dat There are: 258 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Making dummy/rest group for T-Coupling containing 1290 elements Making dummy/rest group for Acceleration containing 1290 elements Making dummy/rest group for Freeze containing 1290 elements Making dummy/rest group for Energy Mon. containing 1290 elements Making dummy/rest group for VCM containing 1290 elements Number of degrees of freedom in T-Coupling group rest is 1545.00 Making dummy/rest group for User1 containing 1290 elements Making dummy/rest group for User2 containing 1290 elements Making dummy/rest group for XTC containing 1290 elements Making dummy/rest group for Or. Res. Fit containing 1290 elements Making dummy/rest group for QMMM containing 1290 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... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 175x175x175, spacing 0.115 0.115 0.115 writing run input file... -- It says, System has non-zero total charge: -2.58e-01. What could be the problem. I tried to solve it, but I can't. what resulted the error? I paste my top and itp files below. sincerly, Jestin - topol.top #include "ffoplsaa.itp" #include "tip5P.itp" [ system ] Pure water [ molecules ] SOL 258 tip5P.itp file --- [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1 opls_1181SOL OW 1 0 2 opls_1191SOL HW11 0.24 3 opls_1191SOL HW21 0.241 4 opls_1201SOL LP11 -0.241 5 opls_1201SOL LP21 -0.241 [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ;c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)
Re: [gmx-users] Chloroform
Hello Mauro, Please have a look at here, http://www.ime.unicamp.br/~martinez/packmol/ regards Jestin On Thu, 29 Nov 2007 Mauro Puppett wrote : > >Hi all! >I've to run a simulation in a box filled with chloroform. >I'm using GROMACS with amber99 force field but I'm a beginner and I have no >idea about how to set up the box or where to find the topology. >Thanks for your help > > >_ >Organizza le tue foto e condividile con i tuoi amici con Raccolta foto di >Windows Live! >http://www.windowslive.it___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: RE: Re: Re: [gmx-users] Energy minimisation
Dear users, What I see the difference between the .gro file given at the examples in the tutor directory and my own .gro file is that the last lines gives 0.000 0.000 0. in my file and in the examples it is not. I assume it is the dimension of the box, isn' it? I built up the gro file using editconf -f *.pdb file. regards Jestin Mandumpal___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: RE: Re: Re: [gmx-users] Energy minimisation
Dear Gromacs users, Thanks for the messages. Tsjerk, I was not aware that capital letters denote unpolite. I just used them to highlight the problem so others can easily pick out. Thanks for the suggestions as well. I modified the file: *** cpp= /lib/cpp define = -DPOSRES -DFLEX_SPC constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 nstlist= 10 ns_type= grid pbc= xyz rlist = 0.8 coulombtype= pme rcoulomb = 0.8 vdw-type = cut-off rvdw = 0.8 nstenergy = 10 Tcoupl = no Pcoupl = no gen_vel= no * But the message is the same. As Dallas and others mentioned, I attach the last part of myt .gro file * 245SOLLP2 1225 0.977 -0.910 0.116 246SOL OW 1226 0.927 -0.946 0.484 246SOLHW1 1227 0.985 -0.880 0.447 246SOLHW2 1228 0.852 -0.950 0.425 246SOLLP1 1229 0.907 -0.928 0.549 246SOLLP2 1230 0.960 -1.008 0.487 247SOL OW 1231 0.970 -0.641 -0.228 247SOLHW1 1232 1.010 -0.704 -0.169 247SOLHW2 1233 1.006 -0.556 -0.201 247SOLLP1 1234 0.900 -0.642 -0.221 247SOLLP2 1235 0.986 -0.655 -0.295 248SOL OW 1236 0.953 -0.556 0.247 248SOLHW1 1237 1.010 -0.481 0.233 248SOLHW2 1238 1.010 -0.624 0.284 248SOLLP1 1239 0.925 -0.578 0.186 248SOLLP2 1240 0.901 -0.540 0.292 249SOL OW 1241 0.974 -0.356 -0.452 249SOLHW1 1242 1.010 -0.438 -0.485 249SOLHW2 1243 1.010 -0.347 -0.364 249SOLLP1 1244 0.904 -0.359 -0.450 249SOLLP2 1245 0.993 -0.302 -0.493 250SOL OW 1246 0.981 -0.228 0.866 250SOLHW1 1247 1.010 -0.229 0.957 250SOLHW2 1248 1.010 -0.312 0.831 250SOLLP1 1249 1.010 -0.175 0.831 250SOLLP2 1250 0.911 -0.223 0.863 251SOL OW 1251 0.979 -0.053 -0.717 251SOLHW1 1252 0.884 -0.039 -0.721 251SOLHW2 1253 1.006 -0.053 -0.809 251SOLLP1 1254 0.994 -0.114 -0.686 251SOLLP2 1255 1.010 -0.001 -0.682 252SOL OW 1256 0.981 0.286 -0.345 252SOLHW1 1257 1.010 0.289 -0.254 252SOLHW2 1258 1.010 0.369 -0.383 252SOLLP1 1259 0.911 0.281 -0.349 252SOLLP2 1260 1.010 0.232 -0.379 253SOL OW 1261 0.968 0.619 -0.698 253SOLHW1 1262 0.886 0.667 -0.704 253SOLHW2 1263 0.942 0.531 -0.672 253SOLLP1 1264 1.010 0.648 -0.649 253SOLLP2 1265 1.002 0.618 -0.759 254SOL OW 1266 0.981 0.543 -0.103 254SOLHW1 1267 1.010 0.467 -0.054 254SOLHW2 1268 1.010 0.618 -0.051 254SOLLP1 1269 0.911 0.544 -0.110 254SOLLP2 1270 1.010 0.545 -0.167 255SOL OW 1271 0.985 0.378 0.613 255SOLHW1 1272 1.010 0.327 0.690 255SOLHW2 1273 0.890 0.377 0.613 255SOLLP1 1274 1.010 0.348 0.555 255SOLLP2 1275 1.010 0.443 0.617 256SOL OW 1276 0.981 0.516 0.287 256SOLHW1 1277 1.010 0.572 0.215 256SOLHW2 1278 1.010 0.562 0.366 256SOLLP1 1279 1.010 0.453 0.283 256SOLLP2 1280 0.911 0.510 0.287 257SOL OW 1281 0.847 0.408 0.942 257SOLHW1 1282 0.841 0.466 0.866 257SOLHW2 1283 0.941 0.407 0.964 257SOLLP1 1284 0.825 0.344 0.926 257SOLLP2 1285 0.810 0.433 0.996 258SOL OW 1286 0.983 0.951 0.741 258SOLHW1 1287 0.888 0.947 0.746 258SOLHW2 1288 1.001 1.010 0.668 258SOLLP1 1289 1.010 0.888 0.728 258SOLLP2 1290 1.010 0.976 0.800 0.0 0.0 0.0 "out.gro" 1293L, 58138C the system is tip5p water molecule. regards, Jestin Mandumpal___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] Energy minimisation
Dear Justin, I made some changes in my .mdp file, but the result is same. My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used is 8 angstrom. I attach the input file here. ** cpp= /lib/cpp define = -DPOSRES-DFLEX_SPC constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 ns_type= grid rlist = 0.8 coulumbtype= pme rcoulomb = 0.8 vdw-type = cut-off rvdw = 0.8 nstenergy = 10 Tcoupl = no Pcoupl = no gen_vel= no * And the output message is : --- creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 2 bonded neighbours for SOL 258 NOTE: System has non-zero total charge: -2.58e-01 processing coordinates... double-checking input for internal consistency... ERROR: 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. --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: Fatal error: There were 1 error(s) processing your input --- "Stop Drinking My Beer !" (The Amps) -- HOW CAN I SETTLE THIS ISSUE? REGARDS JESTIN ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] Energy minimisation
Dear Justin, It seems, the given link which was directed to a post where I got contents of ENERGY MINIMISATION FILE ".mdp" in my previous mail is not the right one, so I paste its content here. *** Geraudis Mustelier gera at ict.cim.sld.cu Wed Dec 12 20:00:03 CET 2001 * Previous message: [gmx-users] Merging several topology files * Next message: [gmx-users] problem with energy minimization * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi I would like to refine a model obtained with modeling by homology technique from X-ray structures. So, I am treating to do an energy minimization. The parameter values in .mdp file are: ; cpp = /lib/cpp define = -DPOSRES constraints = none morse = no integrator = steep nsteps = 2000 ; ; Energy minimizing stuff emtol = 100 emstep = 0.1 ; nstcomm = 1 ns_type= grid rlist = 1 rcoulomb = 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no *** regards Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Energy minimisation
Dear Justin, Thanks for the response. This is my input file (em.mdp) which contains parameters for doing energy minimisation. cpp= /lib/cpp define = -DPOSRES -DFLEX_ constraints= none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.1 nstcomm= 1 ns_type= grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no MY BOX DIMENSION, 20.1* 20.1* 20.1 ANGSTROM. THIS IS THE THREAD WHERE I COLLECTED THE .mdp FILE FOR ENERGY MINIMISATION. http://www.gromacs.org/component/option,com_wrapper/Itemid,84/ regards Jestin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy minimisation
Dear Gromacs users When I run Energy minimisation using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I received the following error message. ** processing coordinates... double-checking input for internal consistency... ERROR: 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. --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: Fatal error: There were 1 error(s) processing your input --- *** MY BOX DIMENSION IS 20.1 * 20.1 * 20.1 I CHANGED THE RLIST, FOR A LOWER VALUE: STILL THE MESSAGE IS SAME. Note: I copied the .mdp file form the gromacs users list ( DECMEBER 2001) regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] creating .tpr file
Dear Gromacs users, Using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I wanted to build up tpr file for the simulation, but failed to do so. I received the error message : Moleculetype SOL contains no atoms. I paste my top files and .itp file below 1. TOP FILE ** #include "ffgmx.itp" #include "tip5P.itp" [ system ] Pure water [ molecules ] SOL 258 - The itp file is [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1 opls_1181SOL OW 1 0 2 opls_1191SOL HW11 0.24 3 opls_1191SOL HW21 0.241 4 opls_1201SOL LP11 -0.241 5 opls_1201SOL LP21 -0.241 [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ;c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy fromfunct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 #endif Can anyone help me in this regard? Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Moleculetype SOL contains no atoms
The top file is #include "ffgmx.itp" #include "tip5P.itp" [ system ] Pure water [ molecules ] SOL 258 - The itp file is [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1 opls_1181SOL OW 1 0 2 opls_1191SOL HW11 0.24 3 opls_1191SOL HW21 0.241 4 opls_1201SOL LP11 -0.241 5 opls_1201SOL LP21 -0.241 [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ;c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy fromfunct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 #endif Can anyone help me in this regard? Jestin Mandumpal___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Moleculetype SOL contains no atoms
Dear Gromacsians, Using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I wanted to build up tpr file for the simulation, but failed to do so. I received the error message : Moleculetype SOL contains no atoms. I paste my top files and .itp file below 1. TOP FILE ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp
Dear Gromacs users, When I tried to build up .tpr file for running energy minimisation, I encountered some problems: This is the command I used: grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr and I received the following error message: Fatal error: Invalid order for directive system, file ""topol.top"", line 4 --- How can I solve this? regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Creating .ndx for TIP5Pwater
Dear David, I didn't get the desired box length when I tried to use editconf command ( I took the tip5p box from gromacs/tutor directory) . Then, I tried editconf command to generate .gro file using myown water box. It worked!! Still, there is a problem. How can I create .ndx file?- I tried make_ndx -n tip5p_W.pdb, but it resulted in a message: input/output error. Could you suggest an alternative way for builing up ndx files? regards Jestin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: Re: [gmx-usersCreating .top, .gro, .ndx, .itp files for TIP5Pwater
QUESTION WITHDRAWN QUESTION WITHDRAWN ***88 I think, I must use the command editconf *.gro bt dodecahedron d 0.5 o *.gro to generate the box of desired length. I didn't notice this command, hence was the confusion. Sorry for the disturbance and I apologise for the mistake regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater
Thanks David for the reply. I was able to build topology file from the info given in the top directory. In contrast to the .gro file for TIP5P box, containing 516 water molecules, given at the top directory, I need a specific box size with exact number of water molecules (258 in 20.1* 20.1 * 20.1) in order to match the experimental density 0.997 gm/cm3. So, I need to create the .gro file and when I tried to create it with pdb2gmx -o tip5p.pdb, it didn't work as I mentioned earlier!!! How can I build up the .gro file for my water box. regards, Jestin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Creating .top, .gro, .ndx, .itp files for TIP5Pwater
Friends, I would like to simulate a box of water (TIP5P model), with 258 water molecules. When I tried to build up the .top, .gro and .ndx files using the command pdb2gmx -p -i -n -o -f tip5p_W.pdb, I got an error message : input/ output error, program aborted. MY input structure, ie, tip5p_W.pdb contains the co ordinates for the solvent box and therefore I dont need to solvate it again!! Could you suggest the exact way to build up thes files ( .top, .gro, .ndx, .itp ) with a starting structure (.pdb files)? regards, Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GLYCAM (sugars) with TIP5P in GROMACS
Dear GROMACS users, I would like to use Glycam forcefields for sugars with TIP5P water model. Does anyone have experience(GROMACS) simulating using GLYCAM/TIP5P? cheers Jestin Madumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
