Hi All,
I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the
top and below part of the ice surface with solvent (the solvent is tip4p
water), some of water molecules go to inside of the ice layers. I did not
receive any errors, but the coordinate files became messy after salva
I have one water molecule in my gro file as below:
TIP4P
4
1SOL OW1 0.054 0.005 0.022
1SOLHW12 0.009 0.072 0.073
1SOLHW23 0.142 0.041 0.008
1SOL MW4 0.060 0.018 0.026
0.00 0.000 0.000
Dear all,
I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
Dear all,
I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
Dear All,
I would like to simulate water using TIP4P/ice potential. My question is
that how can I generate .gro file for this simulation?
I will use TIP4P/ice topology that is available in SklogWiki, but I cannot
understand how can I generate .gro file for this topology. Can I easily use
TIP4P.gro
aging the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
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>1. TIP4P/ice pdb file (
I try to implement CLYFF in gromacs. I created ffbonded.itp,
ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and
molecule.rtp. I want to simulate Kaolinite, and I try to use pdb2gmx to
create a topology. My first question is that should I create any other
files? seco
Dear users,
I try to implement Clayff forcefield for Kaolinite. I created my force
field (I'm not sure about it), but gromacs couldn't find my force field in
the directory. Here is my forcefield.
ffnonbonded
[ atomtypes ]
; name mass chargeptype sigma eps
HW 1 1.0
==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore
Dear usres,
I try to write clayff forcefield, and I want to simulate Kaolinite. I have
some questions about it.
1) should I write clayff forcefield separately or modify one of the
forcefields in share/top?
2) The directory for clayff forcefield should be included ffbonded.itp,
ffnonbonded.itp, ato
@maillist.sys.kth.se
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. solvate only in the z-direction (gangotri dey)
>2. clayff forcefield
>
> Message: 1
> Date: Tue, 8 Aug 2017 08:37:34 -0400
> From: Justin Lemkul
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] clayff forcefield
> Message-ID: <73598616-91d0-a438-e92c-278cd2ee9...@vt.edu>
> Content-Type: text/plain; charset=utf-8; form
Dear All,
I want to create an index file and select some especial atoms in a surface.
My problem is that I have only one residue for the whole surface. How can I
select the atoms on the surface as a different groups in my index file?
Thank you in advance,
Golnaz
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Gromacs Users mailing list
*
> explain better. Now I have 2 groups in my index file Sol and
> Kaoli(surface). I should select some atoms from the Kaoli. So first I
> define the atoms that I want to select in a seperate group, then I should
> erase these atoms from kaoli parts. Am I right? because I want to freeze
&
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