Re: [gmx-users] run MD in vacuum
This settings work, but version isn't newest. integrator<>=<->md dt<><-->=<->0.001 nsteps<><-->=<->1010 nstxout><-->=<->1 nstcalcenergy<->=<->100 nstenergy<->=<->100 cutoff-scheme<->=<->group pbc<--->=<->no nstlist>=<->0 rlist<->=<->0 ns_type>=<->simple coulomb-modifier<-->=<->none vdw-modifier<-->=<->none rcoulomb<-->=<->0 rvdw<-->=<->0 Tcoupl<><-->=<->V-rescale tau-t<-><-->=<->0.1 tc-grps><-->=<->system ref-t<-><-->=<->298.15 Pcoupl<><-->=<->no -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Entropic effects in PMF at zero distance
The formula (5.283) from PDF manual or (3) in http://manual.gromacs.org/documentation/current/reference-manual/special/free-energy-implementation.html#potential-of-mean-force V(r)=-(n-1)*kT*log(r) is obviously incorrect at r=0 for non singular potential (f.e. if "r" is the distance between COMs of two molecules, one of them having cavity at its center). Resulting PMF must be finite at r=0 in contradiction with formula above. Is right variant for the correction of constraint influence for that case exits in literature? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Obtaining opls forcefield
oplsaa force field is situated in /usr/share/gromacs/top (on my PC) folder in gromacs format. If you want to generate oplsaa topology for non-protein molecule it is very comfortable to use acpype (git clone https://github.com/alanwilter/acpype.git) or Jorgensen server http://zarbi.chem.yale.edu/ligpargen . For protein-like molecules pdb2gmx works. For small molecule oplsaa topology also can be written manually with your chemical intuition about atom types in common groups. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to generate the topology files for beta-cyclodextrin using gmx?
pdb2gmx isn't acceptable for any molecule. Only for proteins and DNA-RNA. β-cyclodextrin is present in atb.uq.edu.au in many variants for force field G54A7FF Or it is quit simple to build β-CD with glycan builder and modeller from charrm-gui.org (7 times connect α glucose with 1-4 link). One drawback is that this tool produces linear or branched glycans , but CD is cyclic. You must edit topology and reproduce AGLC residue 7 times (bonds, pairs, angles, dihedrals). If you trust me I can give you my own coordinates and itp for β-CD in oplsaa and charmm36 FF that I use in work. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Changing mdp options for a restart
http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart I tried to simulate instantaneous perturbation in topology and did everything as in instruction (below). Changing mdp options for a restart If you wish to make changes to your simulations settings other than length, then you should do so in the mdp file or topology, and then call gmx grompp -f possibly-changed.mdp -p possibly-changed.top -c state.cpt -o new.tpr gmx mdrun -s new.tpr -cpi state.cpt to instruct gmx grompp to copy the full-precision coordinates in the checkpoint file into the new tpr file. You should consider your choices for tinit , init-step , nsteps and simulation-part . You should generally not regenerate velocities with gen-vel , and generally select continuation so that constraints are not re-applied before the first integration step. My steps are: gmx grompp -f -p -c 4-daspi-S0.gro -o S0 ; old topology compilation gmx mdrun -v -deffnm S0 ; old run gmx grompp -f grompp-S1.mdp -p topol-S1.top -c S0.cpt -o S1 ; here begins actual part But I got error message from "gmx grompp, version 2019" Error in user input: Invalid command-line options In command-line option -c File name 'S0.cpt' cannot be used for this option. Only the following extensions are possible: .gro, .g96, .pdb, .brk, .ent, .esp, .tpr What is the reason of mistake, or something wrong in manual? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QMMM with GROMACS and DFTB3
It seems that ORCA compatible with latest GROMACS if I correctly understand meaning of "//". Look in CMakeCache.txt file in the installer. //QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess, // orca GMX_QMMM_PROGRAM:STRING=None -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QMMM with GROMACS and DFTB3
Im am also starting to perform QM/MM in GROMACS for dyes in ground and excited states in supramolecules, but didn't decided yet what QM package (MOPAC, ORCA or GAMESS-US) will be. But aware of calculation speed of DFT QM in non-empirical methods for average-size molecules I suppose that needed for MD number of steps (~10^6) willl be completely unaccesible. If ORCA will work with latest GROMACS I shall inform. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QMMM with GROMACS and DFTB3
http://wwwuser.gwdg.de/~ggroenh/qmmm.html or 8.13.1 ORCA and Gromacs chapter in orca4 manual. What will be the speed of calculation? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Solid state barostat
I am trying to simulate amorphous organic solid system with Parrinello-Rahman at P=1 Bar. The maximal dt value which holds molecules together is 0.0008 and it's increasing leads to evaporation. What may be incorrect? Berendsen works well with dt=0.001 but it isn't recommended. mdp options for pressure Pcoupl = Parrinello-Rahman tau_p = 1.0 compressibility = 4.5e-05 ref_p = 1 Water compressibility is used because the real is unknown and their densities are close. May I asc one more question? This system is a cubic box of N=1000 identical molecules. What is the most quick way to calculate pairwise distances between all molecules COM (1000x1000 matrix) in confout.gro file? Now I am repeating 1000 times gmx distances command changing $i in selection file resid $i plus resid 1; resid $i plus resid 2; . . . resid $i plus resid 1000 May be exists the way of doing that in one step. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the energy of the individual molecule
Suppose the trajectory of molecular system with interactions between all molecules. How is to obtain the time dependence of intramolecular energy of the given molecule with unique resname and the total energy of this molecule in the system including intermolecular interactions? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] topology for excited electronic state
I found an answer for my old question in amber tools. As it is possible to input the electronic multiplicity in antechamber with "-m" option, the topology for excited electronic state can be produced in the case then the necessary state has different multiplicity than the ground one. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Does GROMACS write charges?
> >No, because that would be a waste of disk space. Charges are a fixed Then "gmx dipoles" will be incorrect in the analisys of the simulation with variable charges. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Does GROMACS write charges?
Does GROMACS write atomic charges in "trr" or "edr" files during trajectory calculation? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Charges in alchemistry
Of course "free-energy = yes" is written in mdp-file. I didn't notice to paste it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] selections
Greetings. Please help to solve simple task with gromacs selections. Say, I have the box with 1000 identical molecules. How to output the array of "nearest neigbours" (for example by distance between COM <5 Angstroms) for each molecule in the box at the time moment=T. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lambda value for free energy calculation
>when should we consider temperature_lambdas, mass_lambdas,restraint_lambdas? If hamiltonian of the system changes between initial and final states the corresponding part is given in coul-lambdas vdw-lambdas bonded-lambdas restraint-lambdas mass-lambdas temperature-lambdas change the external conditions (state of the thermostat) and used only for simulated tempering ( http://manual.gromacs.org/documentation/2018-rc1/user-guide/mdp-options.html#free-energy-calculations ) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Force field informations
>I would like to know where we would get the force field information in GMX The answer is obvious: read manual (chapter 4 I"nteraction function and force fields" and 4.10 "Force field"). The FF files are situated in /usr/share/gromacs/top (for my PC) and are transparent enouth. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hydration free energy
| Have you tried other FE estimate algorithms (i.e. thermodynamic
>integration, MBAR, etc.). Look into the project "alchemical-analysis". It's
>a python script that will give you some good visualizations on what is
>happening at that last step (it's compatible with GROMACS output files).
>There's an associated paper with it as well.
>
>Also double check that you are somehow not mistakingly leaving on some kind
>of interaction that is blowing up after everything else is decoupled
Indeed it is mistake in my options. No TD method can produce good result with
my data.
I wasn't careful. Now I see in dhdl.xvg for lambda=100 that :
@ s0 legend "dH/d\xl\f{} coul-lambda = 1."
@ s1 legend "dH/d\xl\f{} vdw-lambda = 1."
@ s2 legend "\xD\f{}H \xl\f{} to (1., 0.9800)"
@ s3 legend "\xD\f{}H \xl\f{} to (1., 1.)"
@ s4 legend "pV (kJ/mol)"
0. -30.652721 -425.07281 8.5014482 0.000 1.6549610
0.1000 -47.014614 -6562.4468 131.24881 0.000 1.6555369
0.2000 43.812706 -192491.17 3849.8198 0.000 1.6654193
...
...
...
1999.7000 115.17576 -4.0665294e+11 8.1330511e+09 0.000 1.5883621
1999.8000 -1642.2759 -5.8566267e+12 1.1713242e+11 0.000 1.5835983
1999.9000 3147.2195 -6.4759274e+11 1.2951842e+10 0.000 1.5708131
2000. 1253.8263 -5.8808771e+16 1.1761743e+15 0.000 1.5543262
dH/d vdw-lambda is tremendous which means that soft-core vdw must be used.
And one more question for specialists.
In pdf and online manuals I can't understand phrase about " sc-coul ":
"it is only taken into account when lambda states are used, not with
couple-lambda0 / couple-lambda1 "
But it is impossible to establist lambda-path (which is written in mdp-file as
zero-based vector) without indication of it's initial and final states given by
couple-lambda0/1.
And where is the equation describing sc-coul similar to 4.136-4.138 about
sc-vdw on page 98?
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Re: [gmx-users] hydration free energy
>If there are no vdW and Coul it still calculates the average energy, which >without soft-core technique can be very large when atoms overlap. >You can read >http://www.sciencedirect.com/science/article/pii/S0010465516303411 Eq. (2) and >the following text etc. >You can try a soft-core technique to see if it is better. Am I need to use both sc-alpha and sc-coul in that case or it is enouth to write sc-coul = no ; linear interpolation of Coulomb (none in this case) as in the mentioned tutorial? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hydration free energy
Hi, > >Do you know which values of lambdas are used? >Are you using a soft-core technique? > >Asaf Thanks for discussion. I am waiting already few days for anyfing reply. The technique of calculation in the file job.sh. The value of coul- λ is uniformely increasing from 0 to 1 with the step 0.02 for 50 first λ- steps and in the same way for vdw- λ last 50 λ- steps. The problem is in the last trajectory with λ=1 there are no coulomb and vdw intermolecular interactions with the estimate of the entropy according BAR method S=62204236256674537472.00 kT. The neigbouring state used in BAR with λ=0.99 contains no coulomb and some remaining vdw force. Therefore I consider that overlapping of atoms can't produce this error. It happens only then opposite coulomb charges overcome vdw in nearly decoupled state. Therefore there is no need in soft-core interactions because all coulomb is decupling previously to vdw. I made the search in archive and this problem was discussed sometimes, but didn't found clear answer for my case. Now I decided to run the cycle in the reversed order from decoupled state to real interactions. -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] hydration free energy
Hi. I have calculated deltaG of hydration for my molecule in 101 steps. First
50 steps I decoupled coulomb interactions and last 50 - vdw. After all I
calculated resulting value by the command
gmx bar -f {0..100}/dhdl.xvg -o -oi -oh -b 500 >RESULT
and found such phrase in the output
Temperature: 300 K
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/-
0 1 8.16 0.11 0.34 0.06 0.34 0.06 0.91 0.02
1 2 7.61 0.07 0.21 0.08 0.19 0.07 0.86 0.01
...
...
...
97 98 -0.40 0.02 0.42 0.02 0.55 0.02 0.97 0.01
98 99 -2.11 0.03 1.16 0.03 1.84 0.06 1.75 0.03
99 100 -17.55 0.43 13.60 0.44 62204236256674537472.00
33302891096617504768.00 102.60 10.21
WARNING: Some of these results violate the Second Law of Thermodynamics:
This is can be the result of severe undersampling, or (more likely)
there is something wrong with the simulations.
Please answer what is wrong in my simple algorythm. It is based on tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
with some simplification. All necessary data attached.
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[gmx-users] topology for exited electronic state
It is well documented how to construct topologies for ground states of molecules and ions. My task is to simulate the behaviour of dye (anion) after laser exitation in supramolecular complex. Is it possible with standard gromacs force fields? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx velacc
Hi. This is my first letter to this list, sorry. version: :-) GROMACS - gmx help, 2016.4 (-: Problem with velacc command ( http://manual.gromacs.org/documentation/2016.4/onlinehelp/gmx-velacc.html ). In the folder with calculated long trajectory I input: gmx velacc -f traj.trr -mol -b 10 -e 20 and select necessary group after question GROMACS output: Split group of 147 atoms into 1 molecules trr version: GMX_trn_file (single precision) Last frame -1 time 0.000 Last frame -1 time 1100.000 Not enough frames in trajectory - no output generated. What is wrong in my input and why "Last frame" is printed twice? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
