[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
>> -- gmx-users mailing list gmx-users at gromacs.org
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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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