Hi,
Does anyone know what the units of density are in the output (Gaussian 98
cube format) of the spatial distribution function in g_spatial? Is it a
number density or a mass density? If it is a number density, then I would
guess that the units might be atoms/nm^3, since nm is the unit of lengt
So, I also check the literature, for water, using flexible SPC model, in
Buckingham potential form
How do I use the Buckingham potential form for flexible SPC model?
rewriting the itp for water?
Best
XJ
在 2011年11月15日 下午12:12，xiaojing gong 写道：
> Many thanks
>
>
> 2011/11/15 Mark Abraham
Many thanks
2011/11/15 Mark Abraham
> On 15/11/2011 9:17 PM, xiaojing gong wrote:
>
> ...I am not sure...Do you have some suggestions?
>
>
> No. The two functional forms are incompatible. GROMACS only allows you to
> define one set of nonbonded parameters, so you can only use one functi
On 15/11/2011 9:17 PM, xiaojing gong wrote:
...I am not sure...Do you have some suggestions?
No. The two functional forms are incompatible. GROMACS only allows you
to define one set of nonbonded parameters, so you can only use one
functional form in a given simulation. This is fixed i
...I am not sure...Do you have some suggestions?
在 2011年11月15日 上午11:05，Mark Abraham 写道：
> On 15/11/2011 9:03 PM, xiaojing gong wrote:
>
> Many thanks for reply.
> Another question, If I use Buckingham potential for CNT, and I want to
> simulate CNT and water, shall I also transfer the SP
On 15/11/2011 9:03 PM, xiaojing gong wrote:
> Many thanks for reply.
> Another question, If I use Buckingham potential for CNT, and I want to
> simulate CNT and water, shall I also transfer the SPC.itp from LJ to
> Buckingham potential?
>
> The most important is how to transfer?
> I will appreciate
Many thanks for reply.
Another question, If I use Buckingham potential for CNT, and I want to
simulate CNT and water, shall I also transfer the SPC.itp from LJ to
Buckingham potential?
The most important is how to transfer?
I will appreciate it if you can give me any suggestions.
Best
XJ
2011/11
Many thanks for reply.
Another question, If I use Buckingham potential for CNT, and I want to
simulate CNT and water, shall I also transfer the SPC.itp from LJ to
Buckingham potential?
Best
XJ
2011/11/14 Mark Abraham
> On 15/11/2011 2:00 AM, xiaojing gong wrote:
>
>> Hi dear all,
>> For Buckingh
On 15/11/2011 2:00 AM, xiaojing gong wrote:
Hi dear all,
For Buckingham potential， there is three parameters A B C
In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right?
Manual section 2.2 defines the units, and 4.1.2 defines the functional form.
Mark
--
gmx-users mailing list
Hi dear all,
For Buckingham potential， there is three parameters A B C
In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right?
Best
XJ
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Please search the archive at
http
Jennifer Williams wrote:
A very quick question.
Can someone confirm that atomic coordinates are stored as in the
traj.xtc file in units of nm (as opposed to Angstroms)?
I am trying to figure out whether or not in the g_msd program reads in
nm or Angstroms. The standard output of the xy gra
A very quick question.
Can someone confirm that atomic coordinates are stored as in the
traj.xtc file in units of nm (as opposed to Angstroms)?
I am trying to figure out whether or not in the g_msd program reads in
nm or Angstroms. The standard output of the xy graph is nm2 and ps. I
can'
Dear Chris:
Thank you very much for it!
Best!
Xueming
On Thu, Aug 12, 2010 at 5:33 PM, wrote:
> Dear Xueming:
>
> the word "mol" is short form for "mole"
>
> http://en.wikipedia.org/wiki/Mole_%28unit%29
>
> In the pull code context, it refers to moles of the pulled group.
>
> The force is not
Dear Berk:
Thank you so much for the clarification!!! It is so helpful!
Best!
Xueming
On Fri, Aug 13, 2010 at 4:13 AM, Berk Hess wrote:
>
>
> > Date: Thu, 12 Aug 2010 17:33:09 -0400
> > From: chris.ne...@utoronto.ca
> > To: gmx-users@gromacs.org
> > Subject:
> Date: Thu, 12 Aug 2010 17:33:09 -0400
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Units of k1 in the pulling code
>
> Dear Xueming:
>
> the word "mol" is short form for "mole"
>
> http://en.wikipe
Dear Xueming:
the word "mol" is short form for "mole"
http://en.wikipedia.org/wiki/Mole_%28unit%29
In the pull code context, it refers to moles of the pulled group.
The force is not "applied" to the COM of a cluster. The magnitude of
the force is determined based on the COM distance, and the
Hi there
The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a cluster,
the "/mol" in the units of force means per atom in the cluster, or single
molecule composed of several atoms? Sorry, I don't know the default value of
mol in gromacs. Does that mean per molecule? Besides, the for
- Original Message -
From: Amir Marcovitz
Date: Tuesday, July 6, 2010 17:27
Subject: [gmx-users] Units of the Amber99 parameters
To: Discussion list for GROMACS users
> Hi All,
>
> sorry for the naive question, but perhaps someone can tell me what are the
> unit
Hi All,
sorry for the naive question, but perhaps someone can tell me what are the
units of the VDW parameters (i.e., Sigma and Epsilon of the Lennard-Jones
potential) in Amber force-field?
(I'm not sure if its kjoul/mol or kcal/mol)
Thanks,
amir
--
gmx-users mailing listgmx-users@gromacs.or
Nilesh Dhumal wrote:
Hello,
I am doing normal mode analysis for my ststem.
I run the following command.
g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg
I could genrate the eigenfreq.xvg file.
Can you tell what the units for wavenumber.
It giving the unit [cm\S-1\N].
How can I convert to cm-1?
Hello,
I am doing normal mode analysis for my ststem.
I run the following command.
g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg
I could genrate the eigenfreq.xvg file.
Can you tell what the units for wavenumber.
It giving the unit [cm\S-1\N].
How can I convert to cm-1?
Thanks
Nilesh
--
gmx-u
> Date: Wed, 10 Jun 2009 12:16:16 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] units of eigenvalues of mass-weighted covariance
> matrix
>
> Wang Qin wrote:
> > Dear all,
> > I am confused on the units o
Hi,
Well, as has been pointed out before nm\S2\N stands for nm superscript
2 normal. That is correct for non mass-weigthed covariance analysis.
It's just fluctuation. Why would it be kg/m2 (kg/nm2) for mass
weighted? Look at the equations in the manual. It's
sqrt(mass)*sqrt(mass)*nm*nm, which make
Wang Qin wrote:
Dear all,
I am confused on the units of the eigenvalues calculated from
g_covar of mass-weighted covariance matrix. From the output, it says the
unit is "(nm\S2\N)" but from my understanding, it is supposed to be kg/m2.
Various of the GROMACS analysis tools don't write t
Dear all,
I am confused on the units of the eigenvalues calculated from g_covar
of mass-weighted covariance matrix. From the output, it says the unit is
"(nm\S2\N)" but from my understanding, it is supposed to be kg/m2.
Thanks for advance for any comments.
Regards,
Qin
___
Justin,
Thank you! It's pretty clear now.
Vitaly
JAL> Vitaly Chaban wrote:
>> Justin,
>>
>> So the values in the respective columns are pure and ^2 of
>> the particles of the same kind (no additional operations made)?
>>
JAL> Correct, there is nothing mathematical about the xmgrace syntax.
Vitaly Chaban wrote:
Justin,
So the values in the respective columns are pure and ^2 of
the particles of the same kind (no additional operations made)?
Correct, there is nothing mathematical about the xmgrace syntax.
-Justin
Vitaly
JAL> Vitaly Chaban wrote:
Hello,
Sorry for an eviden
Justin,
So the values in the respective columns are pure and ^2 of
the particles of the same kind (no additional operations made)?
Vitaly
JAL> Vitaly Chaban wrote:
>> Hello,
>>
>> Sorry for an evidently stupid question. I use g_dipoles to calculate
>> the total dipole moment of the cell evolut
Vitaly Chaban wrote:
Hello,
Sorry for an evidently stupid question. I use g_dipoles to calculate
the total dipole moment of the cell evolution.
In aver.xvg the following line is present:
@ s0 legend "< |M|\S2\N >"
@ s1 legend "< |M| >\S2\N"
|M| is a modulus of dipole vector. But what are "\S2
* Vitaly Chaban [2009-01-17 16:18:29 +0200]:
Hello,
Sorry for an evidently stupid question. I use g_dipoles to calculate
the total dipole moment of the cell evolution.
In aver.xvg the following line is present:
@ s0 legend "< |M|\S2\N >"
@ s1 legend "< |M| >\S2\N"
|M| is a modulus of dipole v
Hello,
Sorry for an evidently stupid question. I use g_dipoles to calculate
the total dipole moment of the cell evolution.
In aver.xvg the following line is present:
@ s0 legend "< |M|\S2\N >"
@ s1 legend "< |M| >\S2\N"
|M| is a modulus of dipole vector. But what are "\S2\N"? Is N a number
of par
Michael Brunsteiner wrote:
didn't find anything in the manual or online docu.
Is it kJ/mol/nm^2 ???
Yes - this is the unit for all other forces wrt distances.
if yes, the default values (1000.0) given in the posre.itp
produced by pdb2gmx are a bit on the large side, or are
they not ??
Shru
Michael,
Yes, the units are kJ/mol/nm^2. I think the default values in
posre.itp are designed for something like equilibrating your water
with the protein held rigid or something, so they are pretty big.
(This is not insanely large, though -- keep in mind it's only 10
kJ/mol*A^2).
David
On 1/3
didn't find anything in the manual or online docu.
Is it kJ/mol/nm^2 ???
if yes, the default values (1000.0) given in the posre.itp
produced by pdb2gmx are a bit on the large side, or are
they not ??
cheers
mic
___
Vanessa Oklejas wrote:
Hi All,
A simple question: What are the units for the Leonard-Jones potential
parameters "r"and "epsilon" in the gromacs topology files.
r is the variable, sigma and epsilon are the parameters in equation 4.5
of the manual.
In that equation the ratio of sigma and r i
Hi All,
A simple question: What are the units for the Leonard-Jones potential
parameters "r"and "epsilon" in the gromacs topology files.
Thanks,
Vanessa
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-
Hello gmx-ersI am a little confused about the units for the normal mode eigenfrequencies output by g_nmeig. In a previous post, Berk wrote: "The unit is ps^-2 for mass-weighted, amu ps^-2 for non mass weighted. In the CVS code it is cm^-1, which is written in the xvg file"I have tried both versions
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