[gmx-users] no output dgdl file

Emanuel Birru Emanuel.Birru at monash.edu
Thu Mar 24 03:29:40 CET 2011

Hi Justin,

It good that the issue is solved. As per my experience if you want to do
a series of simulations it is not necessary to use foreign_lambda, for
each simulation we can give different lambda values starting from 0 to
1( from fully interactive to non-interactive) no need of foreign_lamda
and certainly no need of generating dhdl.xvg to calculate FE. I think
-dhdl is an optional it will not be generated just because "free_energy
= yes" is present. The problem with the 4.5.3 is not the problem of
generating dhdl data by using single simulation with all foreign_lambda
values. The problem is with g_bar, when I tried to analyse the dhdl.xvg
output (with all the necessary data in it) using g_bar, it doesn't
function properly. The error is related with the source code. I guess
the main advantage of using 4.5.3 to calculated FE using foreign_lambda
was to avoid running series of independent simulations. May be it is
solved on the newer version 4.5.4., didn't try it yet.



-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 12:54 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] no output dgdl file

Emanuel Birru wrote:
> Hi Justin,
> Sure what you wrote is correct, what I am trying to tell to him is
> 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
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
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:



> Cheers 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] 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
> 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:* gmx-users-bounces at gromacs.org 
>> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Moeed
>> *Sent:* Thursday, 24 March 2011 4:13 AM
>> *To:* gmx-users at gromacs.org
>> *Subject:* [gmx-users] no output dgdl file
>> Hello,
>> I have a little problem with FE output file. Below is the settings
>> also I am including -dgdl in the command I issue but no dgdl (or
>> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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