Dear GROMACS Specialists,
I am working about micelles and have a question about the radius of dry core.
May I ask you to answer me, Please?
In one paper, I saw that the radius of dry core equals "where the density
profiles of water and the surfactant hydrocarbon tails cross and a fraction of
ab
On 5/5/12 10:21 PM, Za Pour wrote:
Dear Justin
I appreciate for your reply.I used -maxwarn option because grompp gave me:
WARNING 1 [file ffbonded.itp, line 2705]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.1418 478900
OK, that's reasonable.
I guess I am not us
Dear Justin
I appreciate for your reply.I used -maxwarn option because grompp gave me:
WARNING 1 [file ffbonded.itp, line 2705]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.1418 478900
I guess I am not using improper in the topology file.my cnt.top file lo
On 5/05/2012 11:39 PM, Marcelo Lopez wrote:
Hi, all, I'm still confused about how to set up 1-4 interaction tables
for tabulated non-bonding potentials when using the -tablep option in
mdrun.
The specific question is:
How must I specify the 1-4 interaction in those tables? How many
columns and w
On 6/05/2012 9:27 AM, Sai Kumar Ramadugu wrote:
Dear Gromacs Users,
I am trying to plot the Ryckaert-Bellemans energy for rotating the
chi1 dihedral of glutamate in protein.
I tried to change the ch1 dihedral from 0-360 degrees at increments of
1 degree and saved the pdbs. Then I used the pdb'
On 6/05/2012 7:10 AM, Andrew DeYoung wrote:
Hi,
I think that Gromacs has two parallelization algorithms as of version 4.5:
domain decomposition (the default) and particle decomposition.
For my research, I am using the particle decomposition algorithm. Thus, I
include the -pd switch when callin
Hi All,
I would like to find the stoichiometry for the chelation of a calcium ion
(Ca 2+) with a citrate ion (citrate 3-), as well as the equilibrium
constant or free energy of calcium-citrate complex formation.
x*Ca2+ + y*citrate3- <=> z*calcium-citrate-complex (x, y, and z are
the stoichio
Dear Gromacs Users,
I am trying to plot the Ryckaert-Bellemans energy for rotating the chi1
dihedral of glutamate in protein.
I tried to change the ch1 dihedral from 0-360 degrees at increments of 1
degree and saved the pdbs. Then I used the pdb's to obtain the
corresponding gro files and a single
On 5/5/12 5:10 PM, Andrew DeYoung wrote:
Hi,
I think that Gromacs has two parallelization algorithms as of version 4.5:
domain decomposition (the default) and particle decomposition.
For my research, I am using the particle decomposition algorithm. Thus, I
include the -pd switch when calling
Hi,
I think that Gromacs has two parallelization algorithms as of version 4.5:
domain decomposition (the default) and particle decomposition.
For my research, I am using the particle decomposition algorithm. Thus, I
include the -pd switch when calling mdrun. However, I am worried that in
one
On Sat, 5 May 2012, Dommert Florian wrote:
On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote:
Interesting discussion indeed. I'm just thinking that there might be
no fundamental difference to other thermostats. There's nothing in the
way that causes the friction, but then again, there's no
On 5/5/12 1:27 PM, Za Pour wrote:
Dear gmx users
I am simulation a system including carbon nanotube+water.I have done these
things:
1. I copied oplsaa.ff folder in my working directory
2. I added following lines to atomname2type.n2t
C opls_995 0 12.011 2 C 0.142 C 0.142
C opls_996 0 12.011 3 C
On 5/5/12 1:22 PM, Yun Shi wrote:
Hello all,
I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor -
Donor - Hydrogen in each line of the last index group.
But I wonder I could I use this index file to monitor each hydrogen bond
specified by these triplets along the t
Dear gmx users
I am simulation a system including carbon nanotube+water.I have done these
things:
1. I copied oplsaa.ff folder in my working directory
2. I added following lines to atomname2type.n2t
C opls_995 0 12.011 2 C 0.142 C 0.142
C opls_996 0 12.011 3 C 0.14
Hello all,
I have used g_hbond with -hbn option to generate a .ndx file that has
Acceptor - Donor - Hydrogen in each line of the last index group.
But I wonder I could I use this index file to monitor each hydrogen bond
specified by these triplets along the trajectory?
Also, I understand that th
On 5/5/12 11:39 AM, Shima Arasteh wrote:
Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27?
Maybe, try it and see. Swiss-Param might also be an option.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MI
Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27?
Cheers,
Shima
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Saturday, May 5, 2012 5:58 PM
Subject: Re: [gmx-users] Topology parameters
On
On 5/5/12 9:39 AM, Marcelo Lopez wrote:
Hi, all, I'm still confused about how to set up 1-4 interaction tables
for tabulated non-bonding potentials when using the -tablep option in
mdrun.
The specific question is:
How must I specify the 1-4 interaction in those tables? How many
columns and wit
Hi, all, I'm still confused about how to set up 1-4 interaction tables
for tabulated non-bonding potentials when using the -tablep option in
mdrun.
The specific question is:
How must I specify the 1-4 interaction in those tables? How many
columns and with what?
My primary goal is to set all the 1-
On 5/5/12 9:21 AM, Shima Arasteh wrote:
Dear gmx users,
I need to define a new residue topology ( Formyl ) in CHARMM27 force field. I
have the formyl parameters for GROMOS. I'd like to know if the residue
parameters are the same in different force fields?
Almost certainly not. Each force f
On 5/5/12 4:01 AM, rama david wrote:
Hi Gromacs Friends,
I am doing the justin-lipid tutorial..Link to the tutorial is ...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
I made the g96_53a6_lipid force field as per the instruction of tutorial..
I have some
On 5/5/12 2:50 AM, rama david wrote:
Hi Gromacs friends,
I completed the justin lipid tutorials upto the three steps ...
While performing the tutorial of lipid written by justin ,
I get following query..
1. As per the tutorials we added the
DPPC chain topology
*; Include DPPC chain top
Please be sure to keep the discussion on the gmx-users list and not my personal
inbox.
On 5/5/12 12:27 AM, Shima Arasteh wrote:
You are right.
Corresponding to the articles related to my project, CHARMM27 is often applied.
I don't have any idea about CHARMM36,because I don't know it at all. A
Dear gmx users,
I need to define a new residue topology ( Formyl ) in CHARMM27 force field. I
have the formyl parameters for GROMOS. I'd like to know if the residue
parameters are the same in different force fields?
Thanks,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.
On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote:
> >> Interesting discussion indeed. I'm just thinking that there might be
> >> no fundamental difference to other thermostats. There's nothing in the
> >> way that causes the friction, but then again, there's no physical
> >> particle that ca
Interesting discussion indeed. I'm just thinking that there might be
no fundamental difference to other thermostats. There's nothing in the
way that causes the friction, but then again, there's no physical
particle that causes the stochastic term in v-rescale, and the
Nosé-Hover particle is not ph
Hi Gromacs Friends,
I am doing the justin-lipid tutorial..Link to the tutorial is ...
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
I made the g96_53a6_lipid force field as per the instruction of tutorial..
I have some queris regarding to these new force field
Hi Milinda,
There are different methods to do Free energy. I am using Thermodynamics
Integration method; hence if you are interested to use TI I am willing to guide
you, but I never use bar method. I did some parametrization so if you float
your topology and mpd files I will give you some idea
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