[gmx-users] no output dgdl file

[Emanuel Birru]

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
file names but it also generate all the necessary files including the
xvg's without the need of using -dhdl.

I would appreciate if you come up with a new solution for him.

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 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:* 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 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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