Fw: [gmx-users] Umbrella Sampling _ pulled ion
Shima Arasteh
shima_arasteh2001 at yahoo.com
Fri Jul 26 17:52:45 CEST 2013
Thanks for your previous replies. All are always beneficial and I appreciate you.
As I see in pullx.xvg file, the third column refers to the distance of pull group and reference group. All around -1.2. Is it sufficient to judge that the US has been performed properly?
Thanks for your suggestions in advance.
Sincerely,
Shima
----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, July 25, 2013 4:25 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion
On 7/25/13 7:52 AM, Shima Arasteh wrote:
> 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?
>
Force and force constant are different. The values in the pullf.xvg file
indicate the magnitude of force required to maintain the position of the
restrained ion. The pullx.xvg will probably be more useful in directly
determining how effective the restraining potential was.
-Justin
> ;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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