Dear Mark,
Thank you very much from your help.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, August 21, 2012 9:45 AM
Subject: Re: [gmx-users] parameters for output control
On 21/08/2012 2:55 PM, mohammad agha wro
On 21/08/2012 4:00 PM, Albert wrote:
Dear:
I am going to calculate the area/lipids for my membane system and I
found that GridMAT for area/lipids calculation is not that reliable
since I calculate by XY/(0.5 lipids number) for the pure well
equilbirated POPC lipids system, my values is 67 w
Dear:
I am going to calculate the area/lipids for my membane system and I
found that GridMAT for area/lipids calculation is not that reliable
since I calculate by XY/(0.5 lipids number) for the pure well
equilbirated POPC lipids system, my values is 67 which is close to
experimental data bu
In the original paper [Comparison of multiple Amber force fields and
development of improved protein backbone parameters], 0.8 nm was used;
but I did find recent papers using 1.0 nm for rvdw. And I myself used
1.4 nm, all without obvious abnormality.
On Mon, Aug 20, 2012 at 10:13 PM, Mark Abraham
On 21/08/2012 2:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response. Yes, I said bad!!!
My question is: For example, when I select -b 8 and Gromacs reads as (in
the last step of reading from output file): Reading frame 13000 time 860040.000
, does it perform the
On 21/08/2012 2:30 PM, Yun Shi wrote:
Hello all,
I am simulating protein-ligand complex with amber99sb force field in
TIP3P water. What would be a reasonable value rvdw? I saw someone
uses 1.0, and I did not find any abnormality when using 1.4 nm for
rvdw, but where can I find the right referen
Dear Justin,
Thank you very much from your response. Yes, I said bad!!!
My question is: For example, when I select -b 8 and Gromacs reads as (in
the last step of reading from output file): Reading frame 13000 time 860040.000
, does it perform the computation untill time= 860040 ps or not? or
Hello all,
I am simulating protein-ligand complex with amber99sb force field in
TIP3P water. What would be a reasonable value rvdw? I saw someone
uses 1.0, and I did not find any abnormality when using 1.4 nm for
rvdw, but where can I find the right reference?
And is this force field parameteriz
That is a very valid point, Mark! and very well said indeed. Yes, you
are absolutely correct that we were in a rush to get to the
"equilibrium" point but it had to be pushed gently.
Thanks,
Sapna
On Mon, Aug 20, 2012 at 7:29 PM, Mark Abraham wrote:
> On 21/08/2012 9:02 AM, Sapna Sarupria wrote:
On 21/08/2012 9:02 AM, Sapna Sarupria wrote:
Thanks Mark.
I also discovered that if I set the value of nstpcoule = 1 explicitly
in my mdp file, it runs with the newer version of Gromacs 4.5.5 which
was not the case earlier.
Yes, default behaviour of this kind of thing has varied over time.
Ag
Thanks Mark.
I also discovered that if I set the value of nstpcoule = 1 explicitly
in my mdp file, it runs with the newer version of Gromacs 4.5.5 which
was not the case earlier.
Can you tell me what this variable does exactly? Will your suggestion
that the initial setup might be faulty still be
On 21/08/2012 8:45 AM, Sapna Sarupria wrote:
Hello All,
I have been having rather bizarre experience with Gromacs and was
wondering if any one can shed some light on what is happening. I am
running simulations of a hydrate + water system (think of hydrate as
ice if you are not familiar with them
Hello All,
I have been having rather bizarre experience with Gromacs and was
wondering if any one can shed some light on what is happening. I am
running simulations of a hydrate + water system (think of hydrate as
ice if you are not familiar with them). So basically I have a simple
solid+liquid sy
On 8/20/12 4:24 PM, Albert wrote:
Dear:
I am going to run a very long time simulation with Gromacs CHARMM36 FF. I am
wondering, is single precision compiled version would be good enough for such
kind of purpose or I should use double precision?
Single precision is adequate for most MD pr
Dear:
I am going to run a very long time simulation with Gromacs CHARMM36
FF. I am wondering, is single precision compiled version would be good
enough for such kind of purpose or I should use double precision?
thank you very much
Albert
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gmx-users mailing listgmx-users@gromacs.org
ht
On Thu, Aug 16, 2012 at 1:57 PM, tarak karmakar wrote:
> Dear All,
>
> In my simulation I want the temperature of the system to be reached at
> 300 K only after 3 ps. But after 3ps I see temperature became 402 K.
> So am I doing any mistake in the '.mdp' file given below?
>
>
> ;temperature coupl
On 8/20/12 1:46 PM, sai nitin wrote:
Dear all,
Recently i performed 10ns protein ligand simulation and also ran 10ns
simulation only for ligand in solvent obtain parameters for g_lie to
determine DGBind values.
I calculated -Elj -Eqq values from ligand only simulation energy
file... this is
Dear all,
Recently i performed 10ns protein ligand simulation and also ran 10ns
simulation only for ligand in solvent obtain parameters for g_lie to
determine DGBind values.
I calculated -Elj -Eqq values from ligand only simulation energy
file... this is where im stuck :(
-Elj = Lennard-Jones
On 8/20/12 1:15 PM, mohammad agha wrote:
Dear Gromacs Users,
I have one problem about the way of computation in the Gromacs with frame and
time. (I work with MARTINI CG)
I have one md.mdp file that the parameters of output control in it is as
follows:
nsteps = 3000
dt = 0.030
; Output co
I believe ORCA is setup to run with a maximum of 8 processors. Try
running with 8 processors.
The MM part can be run with 1 processor, use -NT 1 as part of your mdrun flags.
Ramon
On Mon, Aug 20, 2012 at 11:38 AM, Jouko Virtanen wrote:
>
> I have been running QM/MM simulations with orca, but w
I have been running QM/MM simulations with orca, but with only one cpu per
job. I am now trying to run a QM/MM simulation using 16 cpus. This did
not work, so I decided to simplify and just try to run orca in parallel
first. This did not work either. I would post this on the orca mailing
list,
Dear Gromacs Users,
I have one problem about the way of computation in the Gromacs with frame and
time. (I work with MARTINI CG)
I have one md.mdp file that the parameters of output control in it is as
follows:
nsteps = 3000
dt = 0.030
; Output control
nstxout = 2000
nstvout = 2000
n
Dear Gromacs users,
Morning!
I am using Gromacs 4.5.4 version and tries to use the magic power of
g_tune_pme. However, it cannot be executed with the error in
benchtest.log file:
"mpirun error: do not specify a -np argument. it is set for you."
The cluster I use needs to submit mpirun job thoug
Dear all,
Recently i performed 10ns protein ligand simulation and also ran 10ns
simulation only for ligand in solvent obtain parameters for g_lie to
determine DGBind values.
I calculated -Elj -Eqq values from ligand only simulation energy
file... this is where im stuck :(
-Elj = Lennard-Jones
Dear Gmx Users,
I have output from Umbrella Sampling simulations - PMF curve obtained
by WHAM. I want to create on the plot error bars. I have 20 windows
each corresponding to 80 ns simulation. Shall I create PMF from those
results based for 40-60 ns then 60-80 and plot them? Please help.
Steven
Also important to ask is:
What was your APL *before* you inserted the protein? Was it realistic to
begin with? If not, then start your problem solving there...
On 2012-08-19 06:16:48PM +0200, Albert wrote:
> Dear All:
>
> I am using GridMAT-MD to calculate the area/lipid for my POPC system.
>
Hi,
In addition to the Michael's comments, I saw an interesting poster about
this sort of inclusion for the long-range van der Waals interactions at
the Biophysical Society annual meeting earlier this year. A link to the
abstract for the poster is below. I guess this should become available
i
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