xuji wrote:
Thank you for your help! Mark Abraham.
I make a mistake about the codes which compute the coulomb interactions
in nb_generic.c yestoday. Sorry for it.
And I find that there're some difference between the tabulated coulomb
function and Vanilla cutoff coulomb interaction
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Francesco Pietra wrote:
grep W solvated.gro | wc -l
and use that number in the topology?
I forgot to add that the graphic program uses the above grep command,
I don't understand this statement.
giving the same
Francesco Pietra wrote:
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Francesco Pietra wrote:
grep W solvated.gro | wc -l
and use that number in the topology?
I forgot to add that the graphic program uses the above grep command,
I don't understand this
DMPE.itp file as attached
[ moleculetype ]
; Name nrexcl
DMPE 3
[ atoms ]
; nrtype resnr residuatomcgnrcharge mass
1 H 1DMPE H1 0 0.4000 1.0080;
qtot:0.36
2 H 1DMPE H2 0
There is nothing remarkable here, it looks to be a few changes in atom type
relative to DMPC, a procedure that I know has been used successfully for
DPPC:DPPE mixtures: dx.doi.org/10.1529/biophysj.105.076596
I stand by my previous reply. When analyzing your data, you have to consider
the
I looked through the ffoplsaanb.itp file and see that all the H atoms
except for the following four have zero LJ parameters:
HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine Guanine H-C2
However, in the paper Development and Testing of the OPLS All-Atom
Darrell Koskinen wrote:
I looked through the ffoplsaanb.itp file and see that all the H atoms
except for the following four have zero LJ parameters:
HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine Guanine H-C2
However, in the paper Development and
Hi.
I need to create a topology file for a small organic molecule that is to
interact non- covalently with a DNA duplex. I want to use the amber99 force
field.
I saw on this mailing list that you can use acpypi with antichamber to
create a topology for amber force fields. I got the amber10 tools
Justin A. Lemkul wrote:
Darrell Koskinen wrote:
I looked through the ffoplsaanb.itp file and see that all the H atoms
except for the following four have zero LJ parameters:
HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine Guanine H-C2
However, in
Gunnar Widtfeldt Reginsson wrote:
Hi.
I need to create a topology file for a small organic molecule that is to
interact non- covalently with a DNA duplex. I want to use the amber99
force field.
I saw on this mailing list that you can use acpypi with antichamber to
create a topology for
Gunnar Widtfeldt Reginsson wrote:
Hi.
I need to create a topology file for a small organic molecule that is to
interact non- covalently with a DNA duplex. I want to use the amber99
force field.
I saw on this mailing list that you can use acpypi with antichamber to
create a topology for amber
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying to
impose uni-axial pressure of these molecules using semiisotropic option in
grompp.mdp.
However, as the box seems to distort significantly due to the imposed
pressure which leads to the following error
Another question is, how difficult is it to create the topology for the
molecule by hand for the amber99 force field. Could someone please get me
started on that, if it would be easier. The molecule is a derivative of
cytosine.
I am using GROMACS 4 on Mac OS 10.5
Hi,
I would advise to start
Yongchul Chung wrote:
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying
to impose uni-axial pressure of these molecules using semiisotropic
option in grompp.mdp.
However, as the box seems to distort significantly due to the imposed
pressure which leads
Hello,
I merged two simulation boxes, and now I want to perform a minimization
to remove the problems at their boundary! I have reduced the dt to
0.1 and emstep to 0.1 as well. But still I get the
message
Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision)
I am not sure what you refer to as dt, as there no meaning to time in
EM.
Anyway, I think the easiest way is to remove this ware molecule.
Best,
Itamar.
On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes, and now I want to perform a
minimization
to
Sorry,
That was a big typo(a mis-pasted line)!
What is the suggestion anyway about emstep?
Payman
On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote:
I am not sure what you refer to as dt, as there no meaning to time in
EM.
Anyway, I think the easiest way is to remove this ware
I think it is too small. Try removing the water molecule and repeat
the EM. You might need to remove some molecules before you can
minimise your system.
Itamar
On 26/10/2009, at 10:48 AM, Paymon Pirzadeh wrote:
Sorry,
That was a big typo(a mis-pasted line)!
What is the suggestion
On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Yongchul Chung wrote:
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying
to impose uni-axial pressure of these molecules using semiisotropic option
in grompp.mdp.
However, as
Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes, and now I want to perform a minimization
to remove the problems at their boundary! I have reduced the dt to
0.1 and emstep to 0.1 as well. But still I get the
message
Reading file Ih0001_81_93_204_min.tpr, VERSION
Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes,
Are you sure your error is not here? Inspect your result visually! :-)
All the atoms need to be inside the box and non-overlapping.
Mark
and now I want to perform a minimization
to remove the problems at their boundary! I have
On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Yongchul Chung wrote:
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying
to impose uni-axial pressure of these molecules using semiisotropic option
in grompp.mdp.
However, as
Hi
Thank you for your advice and sorry for disturbing you agian.
I read the cooresponding relevant manual sections, I've known
how to get the parameters of the tabulated funcionns.
But how much is the difference between the direct computation
and the table lookup method is?
For example, I
xuji wrote:
Hi
Thank you for your advice and sorry for disturbing you agian.
I read the cooresponding relevant manual sections, I've known
how to get the parameters of the tabulated funcionns.
But how much is the difference between the direct computation
and the table lookup method is?
Yongchul Chung wrote:
Also note that haphazardly changing the vdwtype or rvdw can have
negative impacts on your simulation, depending on your chosen force
field's sensitivity to these parameters.
Thank you for pointing this out. I am relatively new to this method so
am taking
25 matches
Mail list logo
