Dear gmx-users,
I am using gromacs 3.3.3 for my current simulations. using it i have
already gotten the trajectory file, but i have to do a lateral
pressure analysis. I have come to know through the forum that there is
gromacs 3.0.2. version which has this facility, i have downloaded it.
my
Dear gmx-users,
sorry for this repeated mail, the previous one did not have proper subject.
I am using gromacs 3.3.3 for my current simulations. using it i have
already gotten the
trajectory file, but i have to do a lateral pressure analysis. I have
come to know
through the forum that there i
mohsen ramezanpour wrote:
Dear Dr.Justin
I couldn't find any tutorial for doing free energy cycles with gromacs.
Then I was forced to select Umbrella sampling,I read your toturial and
it was very useful for me.I know it approximately good now.
Please let me know if there are any tutorial for
Hi!
I'm simulating a system containg Glycine zwitterions, Leucine and water (i.e. ZGLY, LEU, SOL).
I have no problems doing the energy minimization.
However, for the production run, I get the error:
"Group LEU not found in index file"
How do I fix this problem?
Regards,
Adam
--
gmx-u
I have performed an annealing simulation from temp 300 K to 0 K and I do not
know how to use g_energy command to give me heat capacity Cv as a function
of time or temperature. could anybody help me please? the version of gromacs
that I have installed is 4-5-3
--
gmx-users mailing listgmx-users
Dear Dr.Justin
I remember I had read this toturial.
I asked in gmx.groups which method can I select if I want to evaluate
binding free energy?
And the answer was Umbrella Sampling!
Besides,
You recommended using free energy cycles in this gmail
I just wanted to know other toturials.
Please let me
Adam Bin Idu Jion wrote:
Hi!
I'm simulating a system containg Glycine zwitterions, Leucine and water
(/i.e./ ZGLY, LEU, SOL).
I have no problems doing the energy minimization.
However, for the production run, I get the error:
/"Group LEU not found in index file"/
How do I fix this problem
mohsen ramezanpour wrote:
Dear Dr.Justin
I remember I had read this toturial.
I asked in gmx.groups which method can I select if I want to evaluate
binding free energy?
And the answer was Umbrella Sampling!
And your reply was that you can't do umbrella sampling efficiently. So the
natur
I have attached the output of demo, and another Okay, I just ran the demo and
kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here
is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2gmx program
Press
St
majid hasan wrote:
I have attached the output of demo, and another Okay, I just ran the
demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx
first, and here is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2
I have attached the output of "demo", and "water" with the message.
I just ran the demo and kept pressing enter whenever it asked me. Demo ran the
pdb2gmx first, and here is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the output of the pdb2gmx pr
majid hasan wrote:
I have attached the output of "demo", and "water" with the message.
I just ran the demo and kept pressing enter whenever it asked me. Demo
ran the pdb2gmx first, and here is what I got.
You seem to have the DISPLAY variable is set, so we will pop up a window with
the outp
Hi Majid,
Maybe it's a good idea to find somebody around that can help you get started
with using linux. You should get acquainted with that before trying to use
some specialized software.
Cheers,
Tsjerk
On Feb 13, 2011 6:38 PM, "Justin A. Lemkul" wrote:
majid hasan wrote: > > I have attached
Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now.
Best,
Majid
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sun, February 13, 2011 9:30:52 AM
Subject: Re: [gmx-users] Output of Gromacs Demo
majid hasan wrot
majid hasan wrote:
Thanks, Justin! Sudo seems to have solved my problem, I do get the
outputs now.
You normally don't want to do any work within the Gromacs installation
directories. For the demo, I suppose it's alright, but sudo is really just a
work-around to write in directories which
Okay, thanks. I will install it again in some other directory.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, February 13, 2011 1:39:16 PM
Subject: Re: [gmx-users] Output of Gromacs Demo
majid hasan wrote:
> Thanks, Justin! Sudo seems to h
Dear all:
I just test the tutrial (
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial)
and my own system, and I fond somthing confused me: If I understand correct,
when lamda is 0 (all atoms on), there should be no difference between trun
on or turn off soft-core potention
I have performed an annealing simulation from temp 300 K to 0 K and I do not
know how to use g_energy command in order to give me heat capacity Cv as a
function of time or temperature. could anybody help me please? the version
of gromacs that I have installed is 4-5-3
--
gmx-users mailing list
On 2011-02-14 06.25, leila separdar wrote:
I have performed an annealing simulation from temp 300 K to 0 K and I do
not know how to use g_energy command in order to give me heat capacity
Cv as a function of time or temperature. could anybody help me please?
the version of gromacs that I have in
19 matches
Mail list logo
