Eric Jakobsson wrote:
npt, but permit the box to change dimensions independently in the
three directions in response to that component of the virial.
Does it really matter whether one uses semiisotropic p-coupling or
independent coupling in x and y? Are there any examples where
semiisotopic
CandyCandy wrote:
Hello!
I am a new beginner of Gromacs. I am trying to use g_potential to
calculate the potential across the membrane. But I only got the 2D
plot (potential vs x axis). Can I get the 3D plot (potential vs x vs
y) by using g_potential?
No, you would have to implement this by
On Mon, 17 Dec 2007 09:02:19 +0100
Jochen Hub [EMAIL PROTECTED] wrote:
Eric Jakobsson wrote:
npt, but permit the box to change dimensions independently in the
three directions in response to that component of the virial.
Does it really matter whether one uses semiisotropic p-coupling or
Hi,
have you checked if there is no water inside the membrane after the
use of genbox?
On Dec 16, 2007 1:35 PM, Mark Abraham [EMAIL PROTECTED] wrote:
pragya chohan wrote:
i started with the lipid coordinates from peter tieleman and removed the
water. then i added water by genbox.
I did
Dear All,
I wish to know that at what temperature range the Gromacs OPLS-AA
parameters are valid? I couldn't find any such information. If anyone
has some idea regarding the lower and upper limit of temperature range
within which the calculations can be done. Since I think that parameters
are
Monika wrote:
Dear All,
I wish to know that at what temperature range the Gromacs OPLS-AA
parameters are valid? I couldn't find any such information. If anyone
has some idea regarding the lower and upper limit of temperature range
within which the calculations can be done. Since I think that
Hello!!
I have asked this question since I want to do simulation at 480K to look
for high-temperature behavior. Will it be correct if I simulate at this
temperature??
Thanking you,
Regards,
Monika
David van der Spoel wrote:
Monika wrote:
Dear All,
I wish to know that at what temperature
ya i removed every water molecule that entered the bilayers. after pr should i
do nvt before doing npt? i am doing position restrain also under npt. Date:
Mon, 17 Dec 2007 11:27:01 +0200 From: [EMAIL PROTECTED] To:
gmx-users@gromacs.org Subject: Re: [gmx-users] problem with npt Hi, have
you
Monika wrote:
Hello!!
I have asked this question since I want to do simulation at 480K to look
for high-temperature behavior. Will it be correct if I simulate at this
temperature??
Thanking you,
Regards,
Monika
It depends on the system (which you do not mention). The FF is made for
room
On Mon, 17 Dec 2007 16:12:28 +0530
Monika [EMAIL PROTECTED] wrote:
Hello!!
I have asked this question since I want to do simulation at 480K to look for
high-temperature behavior. Will it be correct if I simulate at this
temperature??
You have not mentioned what system would be simulated at
Dear Behnoush:
The first three lines of popc.itp is not the problem. I got these in
pope.itp.
Could you attach your input files?
Best regards.
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Please
Farzad,
The force constant is up to you to define in the .ppa file you create for
umbrella sampling.
I ask the question about the 0.5 term because I am using Grossfield¹s WHAM
algorithm and it assumes that the biasing potential used has a 0.5 in front,
but I know for example CHARMM does not
Thank you very much, Jochen!
Candy Date: Mon, 17 Dec 2007 09:09:27 +0100 From: [EMAIL PROTECTED] To:
gmx-users@gromacs.org Subject: Re: [gmx-users] g_potential problem
CandyCandy wrote: Hello! I am a new beginner of Gromacs. I am trying
to use g_potential to calculate the potential
Quoting jayant_jacques [EMAIL PROTECTED]:
Hi all!
I am attempting to simulate a protein with AEDANS and DABMI attached to
modified Cys. I got the .top files and .gro from PRODRG but on attempting
simulations I get the error
Warning: 'DAB' not found in residue topology database,
This is a
I have performed a search of the archive, but am yet to understand the
meaning of inconsistent shifts.
I am using GMX331.
I am simulating a protein structure solved by NMR.
I have performed EM, PR and run the structure out for 500ps of MD before
beginning my production runs.
I am using
Thanks all of you for suggestion. I were to use water-solvated protein
system, so 480K will be quite high for it, so I ll try to choose
temperature ranges within 273-373 K. (Hope I have not wrong!!). I
wondered such temperature because i have seen some references using
temperature 420K or so.
Mitchell Stanton-Cook wrote:
I have performed a search of the archive, but am yet to understand the
meaning of inconsistent shifts.
I am using GMX331.
I am simulating a protein structure solved by NMR.
I have performed EM, PR and run the structure out for 500ps of MD before
beginning my
Hi every body
I read a article that wrote 0.5in equation on gromacs.
please help me about determining of force constant and posistion in umbrella
sampling and in later simulation how do I change them.
-
Be a better friend, newshound, and know-it-all
Hi, how are you!I want to perform a molecular dynamics simulation of a
aminoglycoside antibotic under force field of opls. However, I can't get the
opls
parameter about amino group attached to the pyranose ring. I hope someone will
give me a hand and Thank you in advance!
best wishes
zhuliang
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