[gmx-users] md simulation for magnetic nanomaterials

Dear Sir I know gromacs do some md simulation for biological system. I want to do some md simulation on magnetic nanomaterials. Can you anyone give me some idea which software do md simulation for magnetic nanomaterials. -- *Mohammad Zahidul Hossain Khan Graduate student**Department

Re: [gmx-users] dielectric constant 4

me, because I don't feel like doing my own research" may not look very good > in a manuscript. > > Alex > > > On 8/16/2017 5:14 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear User >> >> Dose anyone know how can I use dielectric constant 4 in mdp for

[gmx-users] dielectric constant 4

Dear User Dose anyone know how can I use dielectric constant 4 in mdp for protein during the simulation? -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085

Re: [gmx-users] npt simulation error

<jalem...@vt.edu> wrote: > > > On 8/15/17 9:22 PM, Mohammad Zahidul Hossain Khan wrote: > >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon-r= 4 >> > > epsilon-r is used to change the relative dielectric

Re: [gmx-users] npt simulation error

; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 4 On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir >> >> I am tryin

[gmx-users] npt simulation error

this problem -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085967165* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/S

[gmx-users] gmx sasa

Gsolv" but I do not know the unit. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085967165* -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] error at nvt equilibrium

1548 and 1547 Cannot make an unambiguous inverse block -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085967165* -- Gromacs Users mailing list * Please

Re: [gmx-users] Error in itp file

ists > >> > >> * 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. > >> > > > > > > > > -- > > Souvik Dey > > Integrat

Re: [gmx-users] Error in itp file

Can you give web server link? I have tried but didn't find. On Aug 3, 2017 5:53 AM, "Souvik Dey" wrote: > Yes, using ACPYPE is pretty simple. They have a web server, where you can > upload your PDB or MOL2 file, provide the charge and multiplicity and it > gives you the

Re: [gmx-users] Error in itp file

Hi Can you tell me, how have you used ACPYPE for itp. On Aug 2, 2017 9:36 AM, "Souvik Dey" wrote: > Hi, > > I just generated an itp file from ACPYPE. However, if I try to add ions it > shows the following error: > > Fatal error: > Syntax error - File FAD.itp, line 3 >

Re: [gmx-users] ligand topology

y, GAFF forcefield and amber forcefields are compatible. gaff > is > > >>> simply amber ff for small molecules. > > >>> You have to get first amber tools. The last release is amber tools 16 > > >>> Get the source code from here : >

Re: [gmx-users] ligand topology

ntechamber for creating the >>> small-molecule >>> parameters >>> >>> later, you can use a nice free program called ACEPYP, made to convert >>> amber >>> parameters to gromacs toplogyget the code from here: >>> >>> https://github.com/t-/a

Re: [gmx-users] ligand topology

o gromacs toplogyget the code from here: > > https://github.com/t-/acpype > > Regards > > > > On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan < > za.par...@gmail.com> wrote: > > > Dear Sir > > > > Thank you very much for yo

Re: [gmx-users] ligand topology

Dear Sir Thank you very much for your reply. Can you give me any link or suggestion that i can learn for amber force field for protein and ligand. On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote

[gmx-users] ligand topology

topology and tip3p water model it gives me the error: atomtype OM not found and when I have tried ff03 with gromos topology and spc water model it gives me the error like: atomtype HW not found. Can anyone help me about it? -- *Mohammad Zahidul Hossain Khan Graduate student**Department

Re: [gmx-users] energy minization mdp

Dear Sir Thank you very much. It is working now. On Fri, Jul 28, 2017 at 4:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear User >> >> I have protein-ligand system. I have basic

[gmx-users] energy minization mdp

in energy minimization mdp file. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085967165* -- Gromacs Users mailing list * Please search the archive at