[gmx-users] Umbrella Sampling _ pulled ion

[Shima Arasteh]

After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly?

;define        = -DPOSRES     
integrator      = md            ; leap-frog integrator
nsteps          =100000         ; 1 * 100000 = 100 ps
dt              = 0.001         ; 1 fs
nstcomm     = 10
tinit       = 0
; Output control
nstxout         = 5000           ; save coordinates every 100 ps
nstvout         = 5000           ; save velocities every 100 ps
nstenergy       = 1000           ; save energies every 2 ps
nstfout     = 5000
nstxtcout   = 5000                ; every 10 ps
continuation    = yes            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
rlistlong       = 1.4
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
vdwtype         = switch
rvdw_switch     = 1.0
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.12          ; grid spacing for FFT
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
ewald_rtol      = 1e-5
optimize_fft    = yes
; Temperature coupling is on
tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
tc-grps         = Protein_POPC Water_Ces_CL        ; two coupling groups - more accurate
tau_t           = 0.5   0.5       ; time constant, in ps
ref_t           = 310   310    ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
pcoupltype      = semiisotropic
tau_p           = 4
ref_p           = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull            = umbrella
pull_geometry   = position
pull_dim        = N N Y
pull_start      = yes 
pull_ngroups    = 1
pull_group0     = POPC
pull_group1     = Ces_ion
pull_init1      = 0.0 0.0 0.0
pull_rate1      = 0.0 0.0 0.00
pull_vec1    = 0 0 1
pull_k1         = 4000      ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 2 ps
pull_nstfout    = 1000      ; every 2 ps
; Velocity generation
gen_vel         = no           ; assign velocities from Maxwell distribution
refcoord_scaling    = com



Would you please let me know your suggestions ?


 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: 
Sent: Wednesday, July 24, 2013 9:41 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion



On 7/24/13 11:53 AM, Shima Arasteh wrote:
> Yes, Thanks.
>
> Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings?

Either the restraint distance is maintained with acceptable sampling around that 
distance (given the force constant) or it's not.

> To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US?
>

It should be pretty easy to see.

-Justin

> Many many thanks for your time and suggestions.
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Wednesday, July 24, 2013 8:05 PM
> Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
>
>
>
> On 7/24/13 11:30 AM, Shima Arasteh wrote:
>> Hi,
>>
>> I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane.
>>
>> In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file:
>> pull_group1     = Ces_ion
>>
>> So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) :
>>
>> [ system]
>> ...
>> [protein]
>> ...
>> [protein-H]
>> ...
>>
>>
>> [ Ces_ion ]
>> 85563
>>
>> But after running the grompp, I get this fatal error:
>> File input/output error:
>> index_US.ndx
>>
>>
>> Would you please let me know how I would be able to define a new group for a specific ion ?
>> Did I make a mistake in defining a new group?
>
> What you did in terms of index group content is fine.  The error message means
> that the file called "index_US.ndx" is not present in the working directory, or
> it has the wrong permissions.
>
> -Justin
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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