Hi,
I'm wondering if the version of the intel toolchain loaded when calling
mdrun affects results? My gromacs version was compiled with intel/2015b -
would it matter if module intel/2016b was loaded at runtime?
Thanks
Dries
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Hi GROMACS users,
I have some questions:
1- Can I model a carbonnanotube (CNT) conveying fluid in GROMACS
subjected to a magnetic field?
2- How can I check the centerof mass velocity of my system?
3- I want to calculate volumeand water self diffusion coefficien
Your umbrellas are not well spaced. There is a gap at 1.2, 2.25 and around
4.4 which is affecting your pmf profile.
Add more simulations at those points and re-check again.
Regards,
Sarath
On 22 February 2016 at 11:09, Nikhil Maroli wrote:
> Hello ,
>
> can anyone tell me why im getting profi
Hello ,
can anyone tell me why im getting profile like this after umbrella
simulation
im attaching both hist.xvg and profile.xvg plot
histo plot
https://drive.google.com/file/d/0BxaQk_pcR9viaGRNQlhrcVVmazQ/view?usp=sharing
profile
https://drive.google.com/file/d/0BxaQk_pcR9viMHNOTE5Ba3VlY2c/v
Thank you Mark,
Could you please help to give more instructions on how to generate restraints
on a centre of mass virtual site? I know genrestr can implement restraints, but
I have no idea how to set a virtual site.
BTW: is the latest version suitable for mpt 2.13? it seems that version 5.0.4
Hi Justin,
Thanks for your information. My atom group contains only 3 atoms, each of which
is on one chain of a triple helix. Flat-bottomed is new for me. I went through
section 4.3.2 in the manual, but still feel confused about how to get the
parameters and how to apply constraints. Do you thi
Or probably on a centre of mass virtual site.
Mark
On Sun, 21 Feb 2016 21:27 Justin Lemkul wrote:
>
>
> On 2/20/16 10:44 PM, Ming Tang wrote:
> > Dear Gromacs experts,
> >
> > Is there a approach to fix the centre of mass of a group of atoms only
> without fixing all of the atoms during a stret
Thank you Justin,
do you know how I can find or modify the center of mass velocity of my system?
On Sunday, February 21, 2016 11:50 PM, Justin Lemkul
wrote:
On 2/21/16 3:15 PM, mohammad r wrote:
> Hi everybody,
>
>
>
> Is it correct to say the potential energy after energyminimization
On 2/20/16 10:44 PM, Ming Tang wrote:
Dear Gromacs experts,
Is there a approach to fix the centre of mass of a group of atoms only without
fixing all of the atoms during a stretching process?
No, but you can approximate such behavior using a flat-bottom position restraint
on judiciously c
On 2/20/16 11:16 PM, Irem Altan wrote:
Hi,
Is there a way to generate position restraint files such that the main chain
atoms and the side chain atoms have different force constants? Similarly,
Yes, you can invoke genrestr with a suitable index group for whatever part of
the protein you wan
On 2/21/16 4:14 AM, Negar Parvizi wrote:
Thank you so much for your help.
Should I use protein-ligand complex tutorial for MD simulation of docked
complexes?
Unless the "ligand" is a polypeptide or some other biological molecule that is
described in the force field, yes, that's pretty muc
On 2/21/16 5:44 AM, khourshaeisha...@mech.sharif.ir wrote:
p { margin-bottom: 0.1in; line-height: 120%; }a:link { }
Dear Justin
first of all, thanks for your replay. but I should cite that the bizarre
character that you saw in my Email was Sharif university Email domains
On 2/21/16 8:28 AM, Nikhil Maroli wrote:
Dear all,
i am doing Umbrella sampling,as my ligand is in x axis after i made a
box,so i have to pull it towards -x direction instead of z which mention in
tutorial, can i give
pull_coord1_rate= -0.01
negative rate? is it make any sense or is the
On 2/21/16 3:15 PM, mohammad r wrote:
Hi everybody,
Is it correct to say the potential energy after energyminimization should be
negative and in the order of 105-106 ?according to gromacs tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
Hi everybody,
Is it correct to say the potential energy after energyminimization should be
negative and in the order of 105-106 ?according to gromacs tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
Thank you, Mohammad.
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Gromacs Users m
Thank you very much Justin
On Saturday, February 20, 2016 10:53 PM, Justin Lemkul
wrote:
On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file of my systems. Can you please take a lo
I've shared an item with you:
Screenshot from 2016-02-21 18:45:00.png
https://drive.google.com/file/d/0BxaQk_pcR9viTURiNWVJR3NfS3M/view?usp=sharing&invite=CLDlkagE&ts=56c9bb79
It's not an attachment -- it's stored online. To open this item, just click
the link above.
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Gromacs Users mailing
Dear all,
i am doing Umbrella sampling,as my ligand is in x axis after i made a
box,so i have to pull it towards -x direction instead of z which mention in
tutorial, can i give
pull_coord1_rate= -0.01
negative rate? is it make any sense or is there any ohter method to pull in
-X direction
i
p { margin-bottom: 0.1in; line-height: 120%; }a:link { }
Dear Justin
first of all, thanks for your replay. but I should cite that the bizarre
character that you saw in my Email was Sharif university Email domains
fault not me. also different copies of Email was because of th
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