Re: [gmx-users] Regarding DispCorr

Thank you so much Sir for clearing my doubts. I understood your point. On Mon, Feb 20, 2012 at 12:51, Mark Abraham wrote: > On 20/02/2012 4:19 PM, bipin singh wrote: > >> Thanks for your help. But I am getting different results for potential >> energy when minimization done applying DispCorr=Ene

Re: [gmx-users] Regarding DispCorr

On 20/02/2012 4:19 PM, bipin singh wrote: Thanks for your help. But I am getting different results for potential energy when minimization done applying DispCorr=EnerPres and minimization done without DispCorr. Please provide your suggestions They will be different, but they are highly unlikely

Re: [gmx-users] Using CHARMM force fields in Gromacs, pt. 2

On 20/02/2012 4:56 PM, Jernej Zidar wrote: Hi. Several months ago I was asking how to import and use two CHARMM forcefields in Gromacs at the same time in MD simulations. The two forcefields are CGENFF and CHARMM36. I was able to add the polymer monomers and relevant parameters so I can n

Re: [gmx-users] Re: Using CHARMM force fields in Gromacs, pt. 2

On 2012-02-20 02:53:46PM +0800, Jernej Zidar wrote: > Hi. > Thanks for the advice. > > Putting those two files (i.e. ffbonded.itp and ffnonbonded.itp) > together with the main CHARMM36 forcefield would also mean adding the > missing atomtypes (i.e. the ones from CGENFF) to the atomtypes.dat of

[gmx-users] Re: Using CHARMM force fields in Gromacs, pt. 2

Hi. Thanks for the advice. Putting those two files (i.e. ffbonded.itp and ffnonbonded.itp) together with the main CHARMM36 forcefield would also mean adding the missing atomtypes (i.e. the ones from CGENFF) to the atomtypes.dat of CHARMM36, right? There's no need to patch the forcefields.da

Re: [gmx-users] Using CHARMM force fields in Gromacs, pt. 2

Make a copy of the original Charm36.ff (to say, charmm36cgen.ff) then patch your cgenff conversion into it. To keep things sane, I contained my cgenff conversion into its own ffbondedcgen.itp/ffnonbondedcgen.itp and included those .itps into the charmm36cgen.ff/forcefield.itp I also created separ

[gmx-users] Using CHARMM force fields in Gromacs, pt. 2

Hi. Several months ago I was asking how to import and use two CHARMM forcefields in Gromacs at the same time in MD simulations. The two forcefields are CGENFF and CHARMM36. I was able to add the polymer monomers and relevant parameters so I can now create a pair of top/gro files directly usin

Re: [gmx-users] Umbrella_pull_simulation

Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you

Re: [gmx-users] Regarding DispCorr

On 20/02/2012 2:23 AM, bipin singh wrote: Hello, Thanks for reply. As given in the manual, If we give DispCorr=EnerPres it will apply long range dispersion corrections for Energy and Pressure. But I don't know whether it is logical to apply this during energy minimization. Manual 4.8 sets out s

Re: [gmx-users] Regarding DispCorr

Hello, Thanks for reply. As given in the manual, If we give DispCorr=EnerPres it will apply long range dispersion corrections for Energy and Pressure. But I don't know whether it is logical to apply this during energy minimization. On Sun, Feb 19, 2012 at 20:20, Mark Abraham wrote: > On 19/02/201

Re: [gmx-users] Regarding DispCorr

On 19/02/2012 11:21 PM, bipin singh wrote: Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. What does it do? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch

[gmx-users] Regarding DispCorr

Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

Re: [gmx-users] a question about force fields

On 19/02/2012 7:26 PM, Banafsheh Mehrazma wrote: Dear Mark Thanks for your reply You said "These should function the same", are results of parm 99 and amber 99 the same? Please explain more about (but you should check yourself that each cites the same literature). Random files that you find

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Re: [gmx-users] a question about force fields

Dear Mark Thanks for your reply You said "These should function the same", are results of parm 99 and amber 99 the same? Please explain more about (but you should check yourself that each cites the same literature). One more thing, I want to transfer Force Constant Kθ (kcal/ mol rad2) and Equili