[gmx-users] no output dgdl file

[Moeed]

> Hi Justin,
>>
>
I was looking all the time for a file with dgdl extension throughout the
directory. IIRC in previous versions -dgdl would generate such extension. I
found now .xvg file which has dhdl data. (if I am right dgdl is the very
dhdl in 4.5.3!)



> 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).
>>
>>
> How long has the simulation been running?  Output is buffered, and I find
> that dhdl.xvg is not updated often.
>
>
>  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
>>
>
> Note that turning off all interactions simultaneously (especially when
> using soft-core) can be very unstable.  You should (de)couple vdW and
> Coulombic interactions separately.
>

Yes I read your comment about decoupling separately earlier on but I was not
sure if this could depend upon the system so I was thinking of comparing
results from two trials:

trial 1:
couple-lambda0       =   vdw-q
couple-lambda1       =   none

 trail 2 A:
couple-lambda0       =   vdw-q
couple-lambda1       =   vdw
 trail 2 B
couple-lambda0       =   vdw
couple-lambda1       =   none

So:

1- Does this decoupling issue depend on the system or it is a must for all
FE studies?
2- I actually went through many of FE posts and never found how separete
decoupling can be done. from  trail 2 A and B I get dgdl files but how to
get total vdw-q to none from these two? Please shed some light on the
details of procedure..

3- With free_energy turned off my runs take only a few hours but as I shift
to free_energy          =   yes, runs take nearly one day foe each lambda..
Is this normal for s system having 2500 atoms?

 Thanks

>
>>
>> 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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