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
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed
*Sent:* Thursday, 24 March 2011 4:13 AM
*To:* gmx-users@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
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
ed
*Sent:* Thursday, 24 March 2011 4:13 AM
*To:* gmx-users@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
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
:13 AM
*To:* gmx-users@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
-users-boun...@gromacs.org] On Behalf Of Moeed
Sent: Thursday, 24 March 2011 4:13 AM
To: gmx-users@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
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
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
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