Well, Dr. Lemkul, I tried using:
gmx trjconv -pbc whole
on the .trr file of my previous output. But, running the dipoles command on
this new whole molecules system doesn't give any different results. The value I
get is exactly the same. So, what is to be done? Thanks in advance.
Thejus K
vg -d dipdist.xvg -P 1 -corr mol -c dipcorr.xvg
Can you tell me where I'm going wrong? And also, if I add the additional option
of -epsilonRF 78 with it, the value shoots up to more than 200. How come?
Many thanks,
Thejus Kartha
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Thank you. I am using 5.1.2 version, maybe that's why. Let me check this out.
On Saturday, 15 October 2016 9:20 PM, David van der Spoel
wrote:
On 15/10/16 10:02, Thejus Kartha wrote:
> Greetings!
> I was trying to calculate the dielectric constant of my system (1,4-dio
you please let me know where I am going wrong? I understand that there's
something called the reaction field epsilon value, which is where I could have
gone wrong, as I did not specify it in the first command.
Thanks in advance,Thejus Kartha.
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you could suggest?
On Monday, 10 October 2016 6:14 AM, Justin Lemkul wrote:
On 10/9/16 8:26 PM, Thejus Kartha wrote:
> I'm sorry Dr. Lemkul. I thought I put the links for the images I uploaded on
> Google Drive. Let me try it again.
> The single molecule:
> https
harge, is
there?
Thank you.
Thejus Kartha
On Monday, 10 October 2016 5:47 AM, Justin Lemkul wrote:
None of your screenshots work; most users receive mail in plain text. If you
want to share files or images, upload them somewhere and provide a link.
> [ atoms ]
> ; nr
why gmx genconf shouldn't be just duplicating the
molecule I give it.
The command I used:
gmx genconf -f dioxane.gro -o diox.gro -nbox 8 8 8 -dist 0.3 -shuffle -rot
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Screenshot from 2016-10-10 05-12-09.png
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Thanks
Hello there!
Can you tell me what the difference between using the editconf command with a
-box option to change my box dimensions and manually opening the .gro file and
editing the box vectors at the bottom?
Thanks and regards,
Thejus Kartha
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at my topology more
closely, and what am I to look for here? I mean, what part of the topology
reflects my hydration free energy, or any other material property for that
matter?
On Wednesday, 5 October 2016 6:11 PM, Justin Lemkul wrote:
On 10/5/16 8:37 AM, Thejus Kartha
ecules ]
; Compound #mols
LIG
512-
If you can't find anything wrong with it, I guess I should redo my genconf
command. Isn't it?
Thanks & regards,Thejus Kartha
On Monday, 3 October 2016 5:06 PM, Justin Lemkul wrote:
On 10/2/16 10:09 PM, Thejus Kar
Greetings!
I was performing an EM run with an array of dioxane molecules, for which I had
produced co-ordinates from PRODRG. I got the co-ordinates, and made an array of
it, using the gmx genconf module, and corrected my topology file. Then, I
thought I should minimize the energy of this array b
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