[gmx-users] no output dgdl file

Szilárd Páll szilard.pall at cbr.su.se
Fri Mar 25 22:32:23 CET 2011 

> I am a bit confused on the g_bar part, when it says -f expects multiple
> dhdl files. Do we need to run still multiple independent simulations
> using different foreign_lambda values? I do not see why we should run
> independent simulations, if we use for couple-lambda0 and couple-lambda1
> vdw-q and none respectively.
>

As Justin said, you do need multiple simulations. That is because you
need overlap between state lam_i lam_j to sample and estimate the dG
efficiently . If you only have two states, lambda 0 and 1 you will
most probably have a very poor overlap and therefor a poor dG
estimate.

g_bar expects you to provide a set of dhdl (with -f) or edr (with -e)
files corresponding to you individual simulations at the chosen lambda
values and for every lambda it needs the foreign lambdas provided in
the mdp file.

--
Szilárd


> -----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 1:36 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] no output dgdl file
>
>
>
> Emanuel Birru wrote:
>> 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
>
> This is certainly a viable method, but it is thermodynamic integration,
> not BAR.
>  The purpose of lambda/foreign_lambda is to use the BAR method.
>
>> 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
>
> It has always been my experience (in versions 3.3.3 and 4.5.3) that if
> the free
> energy code is activated, this file is written.  I never specify the
> file names
> independently.
>
>> 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
>
> If you suspect a bug, you should report it.  If you don't use
> foreign_lambda,
> you can't use the BAR method.  You're doing TI, not BAR.  They are
> fundamentally
> different, and the analysis for TI is done independently of any Gromacs
> tool.
>
>> 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.
>>
>
> Version 4.5.3 has worked just fine for all free energy calculations I
> have done.
>   Perhaps BAR can be done with a single simulation and multiple
> foreign_lambda,
> but that was not my understanding of the proper procedure (based on some
> posts
> by developers a few months ago).  Multiple simulations, each at "native"
> lambda,
> are conducted with values of foreign_lambda above and below the native
> value at
> some lambda spacing (except for end points).  Invoking g_bar gives the
> total
> DeltaG over all lambda intervals according to the BAR algorithm.
>
> -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 12:54 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
>> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

More information about the gromacs.org_gmx-users mailing list