On 5/28/13 1:01 AM, Ishwor wrote:
Dear all
I want to study the simulation of Carbonmonoxide in water. I have seen the
Lennard Jones parameters, force constant and partial charges of water in the
file spce.itp inherent in gromacs but couldnt get the parameters for CO .I
will be pleased if anyone
Dear all
I want to study the simulation of Carbonmonoxide in water. I have seen the
Lennard Jones parameters, force constant and partial charges of water in the
file spce.itp inherent in gromacs but couldnt get the parameters for CO .I
will be pleased if anyone provide me the LJ parameters (epsilon
On 2012-10-15 05:54:58AM -0400, Justin Lemkul wrote:
>
>
> On 10/15/12 5:45 AM, cuong nguyen wrote:
> > Dear,
> >
> > The top file downloaded from PRODRG did not consist of [atomtypes]. Please
> > tell me how can I add and use this function?
> >
>
> I see no need to change anything about the L-J
On 10/15/12 5:45 AM, cuong nguyen wrote:
Dear,
The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?
I see no need to change anything about the L-J parameters. Is there some reason
you believe them to be incorrect? If you
Dear,
The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?
Best regards,
Cuong
On 15 October 2012 16:43, Peter C. Lai wrote:
> Is there no [atomtypes] section in the top file?
>
> On 2012-10-15 03:53:54PM +0800, cuong nguyen w
Is there no [atomtypes] section in the top file?
On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> Thanks for you email.
> I already had the .gro and .top files from PRODRG. Now I want to reproduce
> these files following the LJ parameters in a published paper (charge, sigma
> and epsilon valu
Thanks for you email.
I already had the .gro and .top files from PRODRG. Now I want to reproduce
these files following the LJ parameters in a published paper (charge, sigma
and epsilon values). I can change the charge in the top file, yet I do not
know how to change sigma and epsilon values.
Best
It's hard to understand your question. What do you mean by "reference
parameters"? You said you already obtained a .gro and .top from PRODRG, which
uses the gromos 43a1 forcefield to derive the parameters, so if you need
to change the LJ parameters, edit the top file it gave you.
If you want to r
Thank you very much for your email, Justin.
in case I want to use the reference parameters, which force-field and what
should I do to get the .gro and .top files for this molecule?
Best regards,
Cuong
On 12 October 2012 21:14, Justin Lemkul wrote:
>
>
> On 10/12/12 8:04 AM, cuong nguyen wrote
On 10/12/12 8:04 AM, cuong nguyen wrote:
Dear Gromacs Users,
I got the .gro and .top files of 1-octanol downloaded from PRODRG website.
Please let me know if I can change charge, epsilon and sigma of the
molecule as written in a paper? and How to do?
Atom types from PRODRG rarely, if ever
gh as well.
Hope thats not too confusing.
Stephan Watkins
Original-Nachricht
> Datum: Mon, 20 Feb 2012 17:36:07 + (GMT)
> Von: Lara Bunte
> An: "gmx-users@gromacs.org"
> Betreff: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp
>
>
&
On 21/02/2012 4:36 AM, Lara Bunte wrote:
Hello
I use a charmm force field in gromacs. I almost finished my parametrization
except for Lennard-Jones parameters. For this parameters I want to adopt the
values in the charmm force field for the basic atom types.
In gromacs I have to put this para
Hello
I use a charmm force field in gromacs. I almost finished my parametrization
except for Lennard-Jones parameters. For this parameters I want to adopt the
values in the charmm force field for the basic atom types.
In gromacs I have to put this parameters in the ffnonbonded.itp file in the
ergy wells present at the edge of the hydrogen terminated
graphene sheet. Just looking for your comments and thoughts.
Thanks.
Darrell
Date: Sun, 01 Nov 2009 18:20:26 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GRO
a is probably quite consistent.
Doesn't this bring us back to the point of quite a while ago, that an
ammonia model that was probably not parameterized for the gas phase
might not be useful in the gas phase?
Mark
Date: Mon, 26 Oct 2009 08:47:14 +1100
From: Mark Abraham
Subject: Re: [gmx-
atoms?
Thanks.
Darrell
Date: Mon, 26 Oct 2009 08:47:14 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users
Message-ID: <4ae4c762.2060...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1;
arrell
Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users
Message-ID: <4adc1e3a.8010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskin
, all N-H bonds involved hydrogen atoms with
zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or
amine (LYS/LYSH), etc and you will see the atom types used.
-Justin
Thanks.
Darrell
Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Lennard
s
", it appears to me that a site for a non-bonded interaction should
exist on the H atoms within ammonia. Is my interpretation incorrect?
Thanks.
Darrell
Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffopls
Darrell Koskinen wrote:
Hi,
I see that the Lennard Jones parameters for the N & H atoms in ammonia,
represented by opls_127 and opls_128 in the file ffoplsaanb.itp are:
opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01
opls_128 H 1 1.00800 0.340 A
Hi,
I see that the Lennard Jones parameters for the N & H atoms in ammonia,
represented by opls_127 and opls_128 in the file ffoplsaanb.itp are:
opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01
opls_128 H 1 1.00800 0.340 A0.0e+00
0.0e
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