Re: [gmx-users] mdp file of membrane simulation

[Nikhil Maroli]

Hi,
You need to find the resname/index name for the individual component,it
depends on your system. add those names in energygps and do mdrerun
You can find for

PROT-LIPID
PROT-MOLECULE
PROT-REST/WATER
LIPID-MOLECULE
so on
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Re: [gmx-users] demux.pl

[Mark Abraham]

Hi,

IIRC there's not intended to be any difference - you should be able to make
idempotent round-trips by using two rounds of trjcat with the respective
.xvg files. This is potentially useful for large simulation sets where you
don't want to have to store the original trajectories (in case you need
them) and the demuxed ones (because you're using them). But the script
isn't regularly tested, so I would not delete my primary data on the
assumption that it works perfectly...

Mark

On Tue, Oct 11, 2016 at 4:21 PM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
> I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc
> files with demux.pl script. I know we can generate a continue coordinate
> trajectory using "gmx trjcat" combined with "-demux replica_index.xvg"
> option. However I am confused with using the option "-demux
> replica_temp.xvg"  to deal with .xtc files.
>  What kind of trajectories we can get with "-demux replica_temp.xvg", are
> they coordinates at the same temperature?
> Whats the difference between trajectories generated with "-demux
> replica_temp.xvg" and the original output trajectories?
>
> Best regards,
> Ouyang
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[gmx-users] PMF

[Alex]

Dear gromacs user,

I am trying to simulate the PMF a small peptide adsorbed to a solid surface
but no success unfurtunatly.
For some force constant the peptide would not desorbed from the surface and
for higher force constants what you can see in enclosed file will happen.
Some question is:
If it is possible to somehow change the force constant for a coordinate
while pulling step? for example the first 1 ns by by k1 = 5000 and then
reduced to k1 = 1000 for the rest of pulling.

Also, the force constant in the pulling step and umbrella sampling do not
need to be the same necessarily?

How I can improve or increase the number of sampled frame?

 I have enclosed some results as well as mdp file and force in pulling step
in each step below, I would be so appreciated if you could guide me to
improve the results?

PMF result:
https://drive.google.com/open?id=0B_CbyhnbKqQDMC1Ua3BWLUZ3XzA

Force in pulling SMD
https://drive.google.com/open?id=0B_CbyhnbKqQDVWxkd2VLUmozUjg

position in pulling SMD
https://drive.google.com/open?id=0B_CbyhnbKqQDa0VKX0E0Zlp1ODA

Windows-com
https://drive.google.com/open?id=0B_CbyhnbKqQDR0poVlM2RTVSNG8

md-production.mdp
https://drive.google.com/open?id=0B_CbyhnbKqQDdGFRbWQzb29Nbmc

md-pulling.mdp
https://drive.google.com/open?id=0B_CbyhnbKqQDc2NPdlVmSmwydFk

nvt-umbrella.mdp
https://drive.google.com/open?id=0B_CbyhnbKqQDSk9LS2d2Q1pTN2s

npt-umbrella.mdp
https://drive.google.com/open?id=0B_CbyhnbKqQDVnB4STFxeENfREU

md-umbrella.mdp
https://drive.google.com/open?id=0B_CbyhnbKqQDQmFTZWRkR1BkcUE

Thank you very much in advance.

Regards,
Alex
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[gmx-users] demux.pl

[YanhuaOuyang]

Hi,
I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc files 
with demux.pl script. I know we can generate a continue coordinate trajectory 
using "gmx trjcat" combined with "-demux replica_index.xvg" option. However I 
am confused with using the option "-demux replica_temp.xvg"  to deal with .xtc 
files.
 What kind of trajectories we can get with "-demux replica_temp.xvg", are they 
coordinates at the same temperature?
Whats the difference between trajectories generated with "-demux 
replica_temp.xvg" and the original output trajectories?

Best regards,
Ouyang
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Re: [gmx-users] gromacs 2016 vs 5.1.4

[Mark Abraham]

Hi,

As the release notes say,
http://manual.gromacs.org/documentation/5.1.4/ReleaseNotes/index.html, we
fixed bugs. Everybody needs to be able to feel confident that things are
only likely to improve if they move up to a bug fix release, but
acknowledge there will be bigger changes from 5.0, to 5.1, to 2016 versions.

It would be silly to take all the content of 2016 and apply it to 5.1.3 and
call that 5.1.4 :-) Then there would be no point in having a versioning
scheme!

Mark

On Tue, Oct 11, 2016 at 2:09 PM Erik Marklund 
wrote:

> Dear Nikhil,
>
> Use gmx2016. The 5.1.X versions only get bug fixes and a few backports now
> as far as I know.
>
> Kind regards,
> Erik
>
> > On 11 Oct 2016, at 07:19, Nikhil Maroli  wrote:
> >
> > Dear all
> >
> > We have Workstation with GTX 1070 Cards, Which Gromacs I should install
> > Gromacs 2016 or  5.1.4 .. ? , I have seen 2016 is much better but later
> > there was an updated version of v5  ,Would like to get it confirmed.
> >
> > --
> > Regards,
> > Nikhil Maroli
> > --
> > Gromacs Users mailing list
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> posting!
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Re: [gmx-users] gromacs 2016 vs 5.1.4

[Erik Marklund]

Dear Nikhil,

Use gmx2016. The 5.1.X versions only get bug fixes and a few backports now as 
far as I know.

Kind regards,
Erik

> On 11 Oct 2016, at 07:19, Nikhil Maroli  wrote:
> 
> Dear all
> 
> We have Workstation with GTX 1070 Cards, Which Gromacs I should install
> Gromacs 2016 or  5.1.4 .. ? , I have seen 2016 is much better but later
> there was an updated version of v5  ,Would like to get it confirmed.
> 
> -- 
> Regards,
> Nikhil Maroli
> -- 
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