On 10/24/17 12:08 AM, limingru wrote:
Hello Justin, Many thanks for your answer. Another question
is that whether I need adding some Drude particles in my PDB file of DNA or
Protein in the simulation process, if any, how to modify the PDB file? I
pdb2gmx will build everything for you.
have been using the gmx v4.6.5 to do something. I don't know if this version
can run Drude polarizable simulations.
No, you need to check out the developmental version of the code and use
the Drude branch.
-Justin
I am going to do protein interaction with organic solution (e.g. ethanol or
methanol, etc) in Drude2013 force filed using gromacs software. Would you
please give me some warnings? I think it will give me more clear direction and
bring me convenience in simulation process. Thanks a lot.
Best wishes!
--------------------------------
School of Nuclear Sci and Tec,
Beijing Normal University
Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China
----- Original Message -----
From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 162, Issue 88
Date: 2017-10-24 01:10
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Today's Topics:
1. Re: DPD in Groamcs (Goga, N.)
2. Re: Conversion Amber to Gromacs (Thomas Piggot)
3. Re: Conversion Amber to Gromacs (Mark Abraham)
4. Drude polarizable simulations (limingru)
5. Re: Drude polarizable simulations (Justin Lemkul)
6. Doubt about thermostat in MD (Varvdekar Bhagyesh Rajendra)
----------------------------------------------------------------------
Message: 1
Date: Mon, 23 Oct 2017 13:54:20 +0300
From: "Goga, N." <n.g...@rug.nl>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DPD in Groamcs
Message-ID:
<CAAHQ6H62djzjnd=pjzusczz9gvfu9gxtk32ycotdjgcpcis...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Kumar,
Why do you need DPD?
Nicu
On Sun, Oct 22, 2017 at 11:28 PM, Dallas Warren <dallas.war...@monash.edu>
wrote:
Not directly, though one of developers might have better insight into
that. Though there are requests / proposals to add it
https://redmine.gromacs.org/issues/1885
There is DPDmacs http://www.apmaths.uwo.ca/~mkarttu/dpdmacs.shtml
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
On 21 October 2017 at 23:53, praveen kumar <praveen...@gmail.com> wrote:
Dear all
is there any possibility of performing dissipative particle dynamics
(DPD)
in gromacs?
Thanks in Advance
Praveen
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------------------------------
Message: 2
Date: Mon, 23 Oct 2017 12:13:14 +0100
From: Thomas Piggot <t.pig...@soton.ac.uk>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Conversion Amber to Gromacs
Message-ID: <afca89bc-2553-90d1-b2ab-009a4e819...@soton.ac.uk>
Content-Type: text/plain; charset=utf-8; format=flowed
Hi,
The multiplicity/periodicity is the same but always positive in GROMACS.
Kd in GROMACS is the AMBER value multiplied by 4.184 then divided by
IDIVF (the entry after names in AMBER file). The phase is the same.
For more info on why see ambermd.org/formats.html#parm.dat
Cheers
Tom
On 23/10/17 10:09, Elisa Pieri wrote:
Hello again,
sorry I wasn't very clear perhaps..we are trying to modify directly the
ffbonded.itp file (together with all the other interested ones) in the
Amber94 force field in order to include the Amber Lipids17 force field. We
added most of the parameters with no problems (bond equilibrium lengths,
constants, bending and so on), but we were not able to understand what is
the conversion factor for torsion parameters between the Amber software
Suite and Gromacs. I know that in the Amber package, the dihedral force
constant is expressed in Kcal/mol, but I couldn't understand what are the
units (and therefore how to convert the parameters) in Gromacs.
Any idea?
Elisa
On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek <kartheekpi...@gmail.com> wrote:
ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the
appropriate software for converting topologies.
This is the parm.py script I have employed, supply amber topologies
file.prmtop and file.inpcrd as input and amber.save option will give
converted gromacs topologies as output.
import parmed as pmd
#amber = pmd.load_file('prmtop', 'inpcrd')
amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd')
#save a GROMACS topology and GRO file
amber.save('new24_ang.top')
amber.save('new24_ang.gro')
----------------------------------------------
P. Kartheek,
PhD Candidate, Computational Biophysical Chemistry,
Center for Computational Natural Sciences and Bioinformatics,
International Institute of Information Technology,
Marimuthu Krishan Group,
9701577399,
karthee...@research.iiit.ac.in,
On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek <kartheekpi...@gmail.com>
wrote:
You can do with ParmEd
On Oct 20, 2017 10:07 PM, "Elisa Pieri" <elisa.pi...@univ-amu.fr> wrote:
Hello GMX users/developers,
we are trying to add the Amber lipids17 forcefield to the Amber99
forcefield implemented in Gromacs. We are a little bit lost on the
torsion
parameters: how to convert the constant from Amber to Gromacs?
Thank you in advance!
Elisa
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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