[gmx-users] no output dgdl file

[Justin A. Lemkul]

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: 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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