Dear David Sir
Thanks a lot for your help
Sincerely
Rana
On Tue, Jun 19, 2018 at 7:18 PM, David van der Spoel
wrote:
> Den 2018-06-19 kl. 14:52, skrev Rana Ali:
>
>> Dear expert users
>> It will be of great help if somebody share the .mdp file for calculating
>> the surface tension of water
>>
Den 2018-06-19 kl. 14:52, skrev Rana Ali:
Dear expert users
It will be of great help if somebody share the .mdp file for calculating
the surface tension of water
using NVT ensemble
Thank in advance
Regards
Rana
Check: http://virtualchemistry.org/ff.php
--
David van der Spoel, Ph.D., Profes
Dear expert users
It will be of great help if somebody share the .mdp file for calculating
the surface tension of water
using NVT ensemble
Thank in advance
Regards
Rana
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On 5/22/17 6:47 AM, ZHANG Cheng wrote:
Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that
true that NVT needs to change two lines, while NPT and production run only need
to change one line?
Yes.
-Justin
Yours sincerely
Cheng
1) In the NVT:
ref_t =
Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that
true that NVT needs to change two lines, while NPT and production run only need
to change one line?
Yours sincerely
Cheng
1) In the NVT:
ref_t = 370 370 ; reference temperature, one for each grou
You haven't adjusted the temperature on the production mdp file, it's still
300 K.
J
On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote:
> Dear Gromacs,
> I am performing 370 K MD based on Justin's tutorial.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tu
Dear Gromacs,
I am performing 370 K MD based on Justin's tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
After "Step Five: Energy Minimization", I need to do NVT, NPT and a production
run.
I think I need to change 300 K to 370 K in three md
Dear Gromacs users
I had a doubt regarding .mdp options for free energy using constrained
dynamics.
If i wish to change a bond length from l_A to l_B (say for example from 0.5
nm to 5 nm. this bond will be used in the form of constraints type 2.
something similar to what is shown in manual of gr
On 4/4/17 6:21 AM, Matteo Busato wrote:
Goodmorning to everyone,
I'm writing here because I'm trying to perform a calculation about the Enthalpy
of Vaporization of a system with 434 molecules of an ionic liquid. I've already
read all the previous posts in the forum about this subject and it
Goodmorning to everyone,
I'm writing here because I'm trying to perform a calculation about the Enthalpy
of Vaporization of a system with 434 molecules of an ionic liquid. I've already
read all the previous posts in the forum about this subject and it has come
clear to me how to perform the ca
Good morning to everyone,
I am trying to perform a very simple calculation of the free energy of
hydration of a Zinc ion in a box of water, using the slow-growth method and the
gmx_bar program with GROMACS 5.0.4. I've taken the LJ paramethers for Zn2+ from
the Stote and Karplus article dated 1
Dear Justin,
Thank you very much.
Best regards,
Mijiddorj
On 10/20/16 11:47 AM, Mijiddorj Batsaikhan wrote:
> Thank you very much.
>
> *(1)*
> Which one is suitable the following 2 examples for energy groups in my mdp
> file?
>
> *Example 1*
>
> energygrps = Protein Membrane
> energy grps = r
On 10/20/16 11:47 AM, Mijiddorj Batsaikhan wrote:
Thank you very much.
*(1)*
Which one is suitable the following 2 examples for energy groups in my mdp
file?
*Example 1*
energygrps = Protein Membrane
energy grps = r_1 Membrane
energygrps = r_2 Membrane
...
energygrps = r_N Membrane
*Example
h.se
> Subject: Re: [gmx-users] mdp file of membrane simulation
> Message-ID:
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
> You need to find the resname/index name for the individual component,it
> depends on your system. add those names in energyg
Hi
I want to use no constraint in my MD simulation. What will I write in my
mdp file?
Best Regards
Mouri
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Hi,
You need to find the resname/index name for the individual component,it
depends on your system. add those names in energygps and do mdrerun
You can find for
PROT-LIPID
PROT-MOLECULE
PROT-REST/WATER
LIPID-MOLECULE
so on
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Dear users,
I would like to simulate a system that consists of 3 different types of
membrane models, peptides (they contain modified amino acid) and small
molecule. In this case, I would like to know peptide-peptide, peptide-small
molecule, peptide-lipid, and modified amino acid-small molecule
int
tutorials. Got it.
Thank you so much
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: Wednesday, September 2, 2015 12:26 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdp file
On 9/1/15 12:50 PM, Sotirios
On 9/1/15 12:50 PM, Sotirios Dionysios I. Papadatos wrote:
Hi,
I am having some trouble defining a proper mdp file for minimization and
production runs. I am aware of the manual's - site's reference to this matter,
it is pretty thourough.
My question is: How do I know which parameters to us
Hi,
I am having some trouble defining a proper mdp file for minimization and
production runs. I am aware of the manual's - site's reference to this matter,
it is pretty thourough.
My question is: How do I know which parameters to use for each simulation? Is
there a publication, book etc to gui
Dear gromacs users,
I am planing to run a membrane protein simulation with implementation of a
slab geometry, due to ion asymmetry. Below, I just copied the mdp file that
I will be using for NPT equilibration and later, for production run. Can
you please have a look and let me know if there is a n
I'd try
coulombtype = cut-off
rcoulomb = [whatever your vdw cutoff is]
It is my understanding that no grid-based PME will be done and for
(nonexistent in your case) electrostatics, the system will rely on the neighbor
lists created for
your van der Waals interactions. The Gurus will be here soon
Hi,
> On 08 Apr 2015, at 16:28, Mikhail Stukan wrote:
>
> Dear gmx-users,
>
> Could you give me an advice.
> I have a system of uncharged LJ particles. How should the electrostatic part
> of the mdp file look like for the best performance. Is it possible to tell
> GROMACS that it should forge
Dear gmx-users,
Could you give me an advice.
I have a system of uncharged LJ particles. How should the electrostatic part of
the mdp file look like for the best performance. Is it possible to tell GROMACS
that it should forget about electrostatics at all? Or it understands this by
itself and th
On Sun, Dec 14, 2014 at 8:11 PM, Carlos Navarro Retamal
wrote:
>
> Dear Mark,
> Thanks for your quick reply.
> I used this one as a template (provided by one of the tutorials of martini)
>
Tutorials are generally not normative. Some people's tutorials are
deliberately cut down so that they run qu
Dear Mark,
Thanks for your quick reply.
I used this one as a template (provided by one of the tutorials of martini)
> dt = 0.02 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout =
> 1000 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2
> epsilon_r = 15 vdw-type
Hi,
In one sense, there's nothing to do. Set the cut-off scheme to Verlet, and
choose your non-bonded and/or integrator setup according to the
recommendations for your model physics. mdrun's job is to implement it
faithfully, but it's your job to choose it ;-)
Mark
On Sun, Dec 14, 2014 at 7:41 P
Dear gromacs users,
I’mt trying to improve the performance of some CG simulations by using GPU
(with cutoff-scheme = Verlet). So i’m trying to create an specific mdp file for
my simulations (4.6.3 version for now) without luck so far.
Could someone provide me a parameters file? i'll be appreciat
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