Emanuel Birru wrote:
Hi Justin,
Sure what you wrote is correct, what I am trying to tell to him is that
if he has more than one foreign lambda it is better to put all of them
as it is not logical to use only one foreign lambda to calculate FE (0 -
0.1) and he doesn't have delta lambda too. -Deffnm is sure all about
You can do a series of simulations at many values of lambda, each specifying
their own foreign_lambda. It seems to me that this method would be more
reliable, but I have not tested simply attempting a single simulation with all
values of foreign_lambda. Using delta_lambda is (from all that I have read) not
reliable, as there are known issues with "slow growth" methods.
file names but it also generate all the necessary files including the
xvg's without the need of using -dhdl.
Whether or not one specifies -dhdl or -deffnm is independent of whether or not
dhdl.xvg (or whatever name) is written. It is controlled purely by the presence
of "free_energy = yes" in the input file.
I would appreciate if you come up with a new solution for him.
As reported by the OP, this issue had been effectively solved already:
http://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html
-Justin
Cheers
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 12:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
Hi,
Your foreign_lambda value is only one, please put all your lambda
values
separated by space and you will get the dhdl file. And make sure that
This is not required. You can specify as many or as few foreign_lambda
values
as you like.
you use -deffnm when you run your mdrun to get all the out put files
by
default.
The -deffnm flag controls the names of the files, not which ones are
written.
-Justin
Cheers,
*From:* [email protected]
[mailto:[email protected]] *On Behalf Of *Moeed
*Sent:* Thursday, 24 March 2011 4:13 AM
*To:* [email protected]
*Subject:* [gmx-users] no output dgdl file
Hello,
I have a little problem with FE output file. Below is the settings and
also I am including -dgdl in the command I issue but no dgdl (or dhdl)
file generates. I dont figure where the problem lies ! (version
4.5.3).
free_energy = yes
init_lambda = 0
delta_lambda = 0
sc_alpha = 0.5
sc-power = 1
sc_sigma = 0.3
foreign_lambda = 0.1
dhdl_derivatives = yes
couple-moltype = Polymer
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = yes
nstdhdl = 10
separate_dhdl_file = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
Best
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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