[gmx-users] no output dgdl file
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 24 04:34:55 CET 2011
Emanuel Birru wrote:
> I have tried the free energy calculation using 4.5.3, but when I run
> g_bar it still gives me the following and do not generate the output
> files.
>
> prod.xvg: 0.0 - 5000.0; lambda = 0.000
> foreign lambdas: 0.000 (125001 pts) 0.000 (125001 pts) 0.010 (125001
> pts) 0.030 (125001 pts) 0.050 (125001 pts) 0.100 (125001 pts) 0.200
> (125001 pts) 0.300 (125001 pts) 0.400 (125001 pts) 0.500 (125001 pts)
> 0.600 (125001 pts) 0.650 (125001 pts) 0.700 (125001 pts) 0.750 (125001
> pts) 0.800 (125001 pts) 0.850 (125001 pts) 0.900 (125001 pts) 0.950
> (125001 pts) 1.000 (125001 pts)
>
> No results to calculate.
>
> I put my mdp file for production run and the output file prod.xvg on
> the following links for your consideration.
>
> http://hydra.pharm.monash.edu.au/md_project/production.txt (mdp file)
> http://hydra.pharm.monash.edu.au/md_project/prod.txt (xvg file)
>
From the above g_bar output and the .xvg file, it seems that lambda=0 is
considered both native and foreign, which probably causes the algorithm to fail.
Note, too, that the results in the first column of the .xvg file (which would
correspond to some weird difference between lambda=0 and lambda=0, which should
not exist!) also seem to be nonsensically high. This is what I mean when I say
weird results from simultaneous (de)coupling of charges and LJ terms. The
systems are not completely stable, yielding weird energies. The result could
also be some bizarre result of lambda=0 being considered native and foreign.
Based on the .mdp file, I don't know how this could have happened, but all signs
point to some sort of problem with the input.
-Justin
> Cheers,
> Emanuel
>
> -----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 2:02 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] no output dgdl file
>
>
>
> 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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