- Original Message -
From: sonali dhindwal
Date: Friday, May 21, 2010 15:38
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, Discussion list for GROMACS users
---
| > hello Jusitn,
> Thanks for your reply
hello Jusitn,
Thanks for your reply,,
I am sending you the link,
so that you can see the changes in the protein, I have specifically
shown that part of the protein, where I am seeing changes,
http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink
Yello
beeta sheets are of the pro
ul
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users"
Date: Thursday, 20 May, 2010, 6:46 PM
sonali dhindwal wrote:
> Hello Gaurav,
> when i did g_rms with structre before energy minimisation as
refrence and strucutr
23 1 1000 1000 1000
>>
>> which is there in posre.itp file, and if these should have value
of 1000
>> 1000 1000 each ?
>>
>
> These default values are typically quite sufficient to restrain the
> structure.
>
> -Justin
Hello Gaurav,
when i did g_rms with structre before energy minimisation as refrence and
strucutre after energy minimisation, it came to be around 0.02.
--
Sonali Dhindwal
--- On Thu, 20/5/10, Gaurav Goel wrote:
From: Gaurav Goel
Subject: Re: [gmx-users] enegry minimisation
To: jalem
1000 1000 1000
>> 21 1 1000 1000 1000
>> 22 1 1000 1000 1000
>> 23 1 1000 1000 1000
>>
>> which is there in posre.itp file, and if these should have value of 1000
>> 1000 1000 each ?
>>
>
> These default values are typically quite s
re.itp file, and if these should have value of 1000
1000 1000 each ?
These default values are typically quite sufficient to restrain the structure.
-Justin
Thanks in advance.
--
Sonali Dhindwal
--- On *Wed, 19/5/10, Gaurav Goel //* wrote:
From: Gaurav Goel
Subject: Re: [gmx-u
1 1000 1000 1000
23 1 1000 1000 1000
which is there in posre.itp file, and if these should have value of 1000 1000
1000 each ?
Thanks in advance.
--
Sonali Dhindwal
--- On Wed, 19/5/10, Gaurav Goel wrote:
From: Gaurav Goel
Subject: Re: [gmx-users] enegry minimisation
To
Dallas B. Warren wrote:
I seem to say this several times per week: in my experience (and in
the
experience of many others who have posted here) the charges and charge
groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG p
> I seem to say this several times per week: in my experience (and in
the
> experience of many others who have posted here) the charges and charge
> groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG page on the
GROMACS websit
emkul //* wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] enegry minimisation
To: "Gromacs Users' List"
Date: Wednesday, 19 May, 2010, 5:45 PM
sonali dhindwal wrote:
> Thanks Justin for your reply.
> Yes I have included solvent i
Wed, 19/5/10, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] enegry minimisation
To: "Gromacs Users' List"
Date: Wednesday, 19 May, 2010, 5:45 PM
sonali dhindwal wrote:
> Thanks Justin for your reply.
> Yes I have included solvent in the protei
> optimize_fft = yes
>> ;
>> ; Energy minimizing stuff
>> ;
>> emtol = 1000.0
>> emstep = 0.01
>>
>> I hope it will help you to guide me further
>> Thanks
>> --
>>
ilto:er...@xray.bmc.uu.se>>/* wrote:
From: Erik Marklund mailto:er...@xray.bmc.uu.se>>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" mailto:gmx-users@gromacs.org>>
Date: Wednesday, 19 May, 2010, 5:3
gt; fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ;
> ; Energy minimizing stuff
> ;
> emtol = 1000.0
> emstep = 0.01
>
> I hope it will help you to guide me further
>
--- On Wed, 19/5/10, Erik Marklund wrote:
From: Erik Marklund
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users"
Date: Wednesday, 19 May, 2010, 5:31 PM
sonali dhindwal skrev:
> Hello All
> This question may sound trivial to many, but as i am n
indwal
--- On *Wed, 19/5/10, Justin A. Lemkul //* wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users"
Date: Wednesday, 19 May, 2010, 5:17 PM
sonali dhindwal wrote:
> Hello All
> Thi
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users"
Date: Wednesday, 19 May, 2010, 5:17 PM
sonali dhindwal wrote:
> Hello All
> This question may sound trivial to many, but as i am new to this field,
> please help.
> I want to ask a question
sonali dhindwal skrev:
Hello All
This question may sound trivial to many, but as i am new to this
field, please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using s
Hello All
This question may sound trivial to many, but as i am new to this field, please
help.
I want to ask a question regarding my previous query of distortion of protein
strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent algorithm,
sonali dhindwal skrev:
Hello All
This question may sound trivial to many, but as i am new to this
field, please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using s
sonali dhindwal wrote:
Hello All
This question may sound trivial to many, but as i am new to this field,
please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
Can you provide a link to your previous post, for
Hello All
This question may sound trivial to many, but as i am new to this field, please
help.
I want to ask a question regarding my previous query of distortion of protein
strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using steepest decent algorithm,
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