gt; From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@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,
&
a = 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,
>>
;> 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 understandin
March 2011 2:35 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Bla
cs.org] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 2:35 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] no output dgdl file
Emanuel Birru wrote:
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
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 fi
-users-boun...@gromacs.org
[mailto:gmx-users-boun...@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 me
[mailto:gmx-users-boun...@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 seri
,
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@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 tha
g_bar gives the total
DeltaG over all lambda intervals according to the BAR algorithm.
-Justin
Cheers,
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 12:54 PM
To: Gromacs U
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 on
://lists.gromacs.org/pipermail/gmx-users/2011-March/059631.html
-Justin
Cheers
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Thursday, 24 March 2011 12:35 PM
To: Discussion list for GROMACS users
Subject:
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 spa
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
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
you use -deffnm when you run your mdrun to get all the out put files by
default.
Cheers,
From: gmx-users-boun...@gromacs.org
[mailto:gmx-use
Moeed wrote:
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!)
The extension h
> 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
Moeed wrote:
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).
How long has the simulation been running? Output is b
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