[gmx-users] more than one peptide in one simulation box

shahid nayeem msnayeem at gmail.com
Tue Apr 27 15:29:10 CEST 2010


My peptide is 26 residue alpha helix obtained from crystal structure  .pdb
file. I am posting energy minimization, position restarint and full MD
simulation .mdp file

Energy minimization

cpp = /usr/bin/cpp

define = -DFLEX_SPC

constraints = none

integrator = steep

nsteps = 3000

;

; Energy minimizing stuff

;

emtol = 1000

emstep = 0.01

nstcomm = 1

ns_type = grid

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.14

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

Tcoupl = no

Pcoupl = no

gen_vel = no
Position_restraint.mdp


cpp = /usr/bin/cpp

define = -DPOSRES

constraints = all-bonds

constraintalgorithm = LINCS

integrator = md

dt = 0.002 ; ps !

nsteps = 25000 ; total 50 ps.

nstcomm = 1

nstxout = 500

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 10

ns_type = grid

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.14

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein Non-protein

tau_t = 0.1 0.1

ref_t = 300 300

; Energy monitoring

energygrps = Protein Non-protein

; Pressure coupling is not on

Pcoupl = no

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is on at 300 K.

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529
Full_MD.mdp

cpp = /usr/bin/cpp

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 5000000 ; total 10000 ps.

nstcomm = 1

nstxout = 5000

nstvout = 40000

nstfout = 0

nstlog = 500

nstenergy = 500

nstlist = 10

ns_type = grid

rlist = 0.9

coulombtype = PME

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.14

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein Non-protein

tau_t = 0.1 0.1

ref_t = 500 500

; Energy monitoring

energygrps = Protein Non-protein

; Isotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is off at 500 K.

gen_vel = no

gen_temp = 500.0

gen_seed = 173529

 shahid



On 4/27/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dear Mark
>> Following your advice I started using three peptide in one simulation box.
>> Iwas able to add these with genconf as previously in ordered manner,
>> generated .gro with genconf, solvated it and after energy minimization I did
>> MD run for 10ns. Everything ran well. In the end when I see the trajectory I
>> find unfolding of the original chain but the two additional peptide
>> introduced through genconf show appearance of new secondary structures. Even
>> in these two the secondary structure do not develop at the same point. Why
>> the three equivalent peptide behave differently in similar environment. How
>> can I explain this observation. why the first peptide does not show any new
>> secondary structure. Sholud I go with higher number of molecule. Will it
>> make any difference if peptides are added in disordered manner and then
>> simulated.
>>
>
> Initial orientation should likely have nothing to do with it.  Perhaps this
> is even the proper behavior for whatever your peptide is.  Is its structure
> dynamic?  Is the size of your peptides large enough to even believe that
> they would be intrinsically stable?  Many model peptides, in isolation, have
> very transient structures.
>
> It could also be that your simulation parameters are poorly chosen, so the
> force field is breaking down.  If you want comments on your .mdp file,
> please post it.
>
> -Justin
>
> Shahid
>>
>>  On 4/23/10, *Mark Abraham* <Mark.Abraham at anu.edu.au <mailto:
>> Mark.Abraham at anu.edu.au>> wrote:
>>
>>    On 23/04/10 13:16, shahid nayeem wrote:
>>
>>        Dear All
>>        I am trying to study inter peptide interaction fpr which I need
>>        to put
>>        more than one peptide in one simulation box. I did it with genconf
>>        command but this inserts peptide in a regular ordered manner I want
>>        these to be in irregular disordered insertion. Even after using
>>        genconf
>>
>>
>>    Well that's a difficult and atypical scenario. genconf -shuffle will
>>    allow you to stack the same peptide in a regular array with random
>>    rotations of the whole box. Then you can solvate, equilibrate and
>>    run MD at a high temperature to give yourself a quasi-disordered
>>    starting state.
>>
>>        , I tried to proceed furthe after solvation with spc water. The
>>        energy
>>        minimization (steepest descent) failed to converge even after
>>        5000 steps
>>        and theirafter position restraint dynamics failed giving
>>        segmentation
>>        fault. Introducing more peptide after generating .gro with -ci
>> -nmol
>>        gives error showing more than one residue in insert molecule.
>>        Please help me and write  commands which I should follow.
>>
>>
>>    No, because that's an impossible task. We can't begin to guess the
>>    reasons for things failing without seeing the actual output (was the
>>    EM energy large and negative? what was the actual error message
>>     from -ci -nmol?).
>>
>>    You should be careful to start with a small test case so that you
>>    can learn the workflow with a manageable problem. Can you get a
>>    single peptide to equilibrate? Two stacked peptides? It is best to
>>    learn to walk before trying to run :-)
>>
>>    Mark
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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