[gmx-users] Simulated tampering using GROMACS software package (protein+membrane)

[Pratiti Bhadra]

Dear User,

I am trying simulated tampering with Gromacs 2018.1

mdp setting with


nstexpanded = 100
simulated-tempering = yes
sim-temp-low = 300
sim-temp-high = 355
simulated-tempering-scaling = linear
init_lambda_state = 0
temperature_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45
0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00

But temperature of simulation is not shifting. it is always 300.
I am pulluzed, what I am doing wrong and what parameters I have to set.

Regards,
Pratiti

-- 
Pratiti Bhadra
Post Doctoral Research Fellow
University of Macau, Macau, China
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Re: [gmx-users] (no subject)

[Pratiti Bhadra]

How many frames do u save using trjconv?. Can you please post your full
trjconv command here.
On 14 May 2016 18:21, "Chalaoux, Francois-Regis" <
francois-regis.chala...@evotec.com> wrote:

> What is your protein, PDB Id ?
>
> FR.
>
> > Le 14 mai 2016 à 12:04:09, Upasana Ray  a
> écrit :
> >
> > yes I have removed water & the pdb file only contains  protein
> >
> > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> > francois-regis.chala...@evotec.com> wrote:
> >
> >> Hi,
> >>
> >> Did you removed Water ?
> >> Check also there is no other protein in the same file.
> >>
> >> FR.
> >>
> >>> Le 14 mai 2016 à 07:04:15, Upasana Ray  a
> >> écrit :
> >>>
> >>> Dear  user,
> >>>
> >>> I have generated my final protein.pdb file by using trjconv command
> from
> >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening
> >> it
> >>> for docking purpose my computer is freezing. Now how can I reduce my
> pdb
> >>> file size  from GB to MB for using it properly. please help me to deal
> >>> with this problem.
> >>> --
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[gmx-users] simulation Self assembly monolayers with OPLS-TIP3P (CPU and GUP)

[Pratiti Bhadra]

Dear All,

I am having a problem with OPLS FF.

If I simulated SAMs layer with only water layer (without any peptide and
protein) using OPLS-AA + TIP3P in GPU system that simulation is simulated
properly there is no problem. But if the same system I run using MPI
(parallel gromacs) then water molecules are penetrating SAMs layer going
toward Sulfure atoms and make a whole in SAM layer. I am confused why both
system is giving me separate result? I want it to run in MPI.

Can anyone solve this problem?

Looking forward.

Regards,
Pratiti
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Re: [gmx-users] radial distribution function of fullerene COM and O of water

[Pratiti Bhadra]

On Dec 29, 2013 8:51 PM, mali 18crow...@gmail.com wrote:

 Hi friends

 Have performed simulation of fullerene and water molecules and calculated
 free energy of solvation. Now want to calculate the radial distribution
 function of fullerene COM and O of water molecules.
 Could you please help how to perform it.
 Thanks in advance

 Mali

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