[gmx-users] no output dgdl file
Moeed
lecielll at googlemail.com
Fri Mar 25 19:22:59 CET 2011
Thank you Justin and Emanuel for helpful remarks. I am a little confused
what is the proper detailed procedure to perform FE using TI and BAR when
decoupling nonboded terms separately. I write down my understanding and
would appreciate your comments.
Summary:
TI: One needs to vary init_lambda (=native) from 0 to 10 (say 0.1
increments) and obtain 11 xvg files. (for simultaneous decoupling)
1- Here foreign_lambda does not make sense as it pertains to BAR.
2- If one intends to do separate decoupling, for each native labmda run two
times with the appropriate couple-lambda0 & couple-lambda1. For each
native lambda we end up with two xvg files. coul-0 to coul-11 and vdw-0 to
vdw-11. (actually I am not sure what is easiest way of summing up two
columns from coul-0 + vdw-0 ... aside from EXCEL..). Move the total sum at
each point to the file total-0 to total 11. Run g_average on each total-?
and perform numerical integration to get delta G or H.
BAR: Run 2*11 times with the following settings for appropriate
couple-lambda0 & couple-lambda1 to get coul-0 to coul-11 and vdw-0 to
vdw-11.
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
Add up coul-0+vdw-0 > total-0 (again I dont know the proper tool for adding
up columns)
.
. (for intermedaite steps there are
3 columns to sum. one before and after native lambda)
.
> total 11
Run g_bar on total-?.xvg files.
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?
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).
Thanks for your help.
>
> 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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