Also, just one more floating query...
In presssure coupling,
Previously, I have been using
tau_p = 1.0
but for this simulaion, I have changed it to
tau_p = 2.0
This was after seeing the mdp file of one of your tutorials. Just wanted to
confirm if that's okay.
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Sorry for the typo.
grompp -f md.mdp -c npt.gro -p complex.top -t npt.cpt -o md.tpr
This is fine, right?
Thanks very much Justin for confirming the mdp file opions..
On Fri, Apr 18, 2014 at 2:11 PM, Justin Lemkul wrote:
>
>
> On 4/18/14, 8:55 AM, Ankita Naithani wrote:
>
>>
;
> On 4/18/14, 4:57 AM, Ankita Naithani wrote:
>
>> Hi,
>>
>> I am trying to run a simulation with the following optins in my production
>> mdp file. Previously I have run the simulations with the production run
>> parameters using V-rescale thermostat and bere
t had any
previous experience with Parinello-Rahman so, any advice would surely help
me.
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Hi Justin,
Thank you very much for your reply. I shall try to work my way around and
see.
Kind regards,
Ankita
On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul wrote:
>
>
> On 3/24/14, 7:57 AM, Ankita Naithani wrote:
>
>> Hi, so I modified my mdp file which now looks
n, Mar 24, 2014 at 11:48 AM, Ankita Naithani
wrote:
> Hi Pavan,
> Thank you for your response. I am trying to generate the tpr file with the
> following parameter;
> ; Neighborsearching
> ns_type= grid; search neighboring grid cells
> nstlist= 5;
give you the same error
>
>
> On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
> wrote:
>
> > Hi,
> >
> > I am trying to run a simulation of my protein (monomer ~500 residues). I
> > had few questions and erors regarding the same.
> > I have previously
-off vdW scheme
; Velocity generation
gen_vel= yes; Velocity generation is on
gen_temp= 318; reference temperature, for protein in K
Kind regards--
Ankita Naithani
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Kind regards,
Ankita
On Tue, Feb 25, 2014 at 1:15 PM, Justin Lemkul wrote:
>
>
> On 2/25/14, 4:54 AM, Ankita Naithani wrote:
>
>> Hi,
>>
>> I was wondering as to what exactly happens during the binning of Free
>> Energy Landscapes as generate
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> *Betreff:* Re: [gmx-users] Bin files of g_sham
> You're not asking it to read the bin index file in your command. Maybe
> that explains what you're seeing?
>
> On 18 Dec 2013, at 13:51, Ankita Naithani
> wrote:
>
> > Hi Lloyd,
> >
> > So, my input to
nt. You
> might be trying to do something else however...
>
> Stephan
> *Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr
>
> *Von:* "Ankita Naithani"
> *An:* "Discussion list for GROMACS users"
> *Betreff:* Re: [gmx-users] Bin files of g_sham
> I wou
go
about that? Could you please help me with that?
Kind regards,
Ankita
On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani
wrote:
> Hi Llyod,
>
> Thank you for your reply. I actually wanted to extract frames
> corresponding to the g_sham output. The input for g_sham in my case was
&g
e's
> also 2 other tools that do this the same way...
>
> Stephan Watkins
> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr
> *Von:* "Ankita Naithani"
> *An:* "Discussion list for GROMACS users"
> *Betreff:* [gmx-users] Bin files of g_sham
>
representative frame corresponding to these time points?
I am a little confused as to what is stored in the bins? Timepoints or
frame number and then alternatively how to get the representative
frame/snapshot stored at that specific bin number.
Kind regards,
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t;
> To compare eigenvectors, make sure that all frames in all trajectories are
> oriented in the same way, using the same or a similar reference structure
> for fitting. Then you can make a comparison like that.
>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Nov 25, 2013 at 1:00 A
> Tsjerk
>
>
> On Sun, Nov 24, 2013 at 2:38 PM, Ankita Naithani
> wrote:
>
> > Hi,
> >
> > I wanted some help regarding vector components. I.e. when we use the
> > g_anaeig command with a flag of -comp, it outputs a file of the
> > corresponding eigenvec
mean? Also, what are the units of these components? Like the
numbers on Y-axis, what are the corresponding units? I would be really
grateful if anyone could kindly help me on this.
Apologies for reposting but was wondering if anyone has any thoughts on it?
Best wishes,
--
Ankita Naithani
mean? Also, what are the units of these components? Like the
numbers on Y-axis, what are the corresponding units? I would be really
grateful if anyone could kindly help me on this.
Best wishes,
--
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