[gmx-users] no output dgdl file

Szilárd Páll szilard.pall at cbr.su.se
Fri Mar 25 22:17:02 CET 2011 

> 1- I am wondering for each interval say
>
> Interval 2:
> init_lambda = 0.05
> foreign_lambda = 0 0.1
>
> how this foreign_lambda 0 is related to the init_lambda = 0 from interval 1
> and the same for foreign_lambda = 0.1 in interval 2 and init_lambda = 0.1 in
> interval 3? Is there a physical meaning?

Intermediate states are non-physical. For the details on how do
intermediate state contribute to the final free energy estimate, see
the original BAR paper [*].

> 2- If one needs to run multiple native lambda for both methods what is the
> adnatage of BAR over TI. I thought using foreign_lambda facilitates FE
> calculations in terms of amount of work but it seems it is only a different
> method (BAR).

Regarding 2), to summarize the advantage of BAR: it's been proved that
it's the best asymptotically unbiased method which the its greatest
strength.

In practice, unlike with TI where in order to sample efficiently you
need containment relationship between the "important" states of B wrt
the important states of A, for BAR good overlap is enough. Also, the
method itself provides with an estimate for overlap which gives a good
indication where you need more lambda points. Again, for details check
[*].

A few more points:
- You don't need all other states as foreign_lambda for a certain
lambda, but if you put them all there it won't hurt, but it will
increase your runtime. A rule of thumb often used is to use as foreign
lambdas a few lambda values around the respective lambda.
-  There is a very handy feature which makes possible writing the free
energy data to the binary edr files (separate_dhdl_file = no mdp
option). The advantages are much faster processing with g_bar and way
less disk usage (note that you can write energy frames relatively
rarely if you wish, while sampling the dhdl more often).


[*] Bennett, Efficient estimation of free energy differences from
Monte Carlo data; JCP (1976); 22:(2), 245-268.

--
Szilárd

>>
>>
>> Emanuel Birru wrote:
>>>
>>> Yeah, I am using IT and do analyse the result using another method not
>>> bar. But I used g_bar when I was using the foreign_lambda and simulate
>>> all in a single file. I have already sent my suspect few weeks back.
>>
>> Is there an active redmine issue?  I cannot find any post from you in the
>> list archive from the last few months.  What is the issue?
>>
>>> 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 I mentioned to the OP of this thread, simultaneous (de)coupling of vdW
>> and Coulombic interactions is not stable.  The output energies are not
>> trustworthy, in my experience due to physically unreasonable configurations
>> and the potential for numerical singularities.
>>
>> The multiple files that g_bar expects are not simply from two separate
>> processes, however.  It expects dhdl.xvg files from multiple values of
>> native lambda that have corresponding foreign_lambda values in it, i.e.:
>>
>> Interval 1:
>> init_lambda = 0
>> foreign_lambda = 0.05
>>
>> Interval 2:
>> init_lambda = 0.05
>> foreign_lambda = 0 0.1
>>
>> Interval 3:
>> init_lambda = 0.1
>> foreign_lambda = 0.05 0.15
>>
>> etc.
>>
>> -Justin
>>
>>> For IT I am using 4.5.3 and it is working good so far.
>>>
>>> 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 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
>>
>> ========================================
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