AW: cell size

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Dec 15 2011 - 00:16:59 CST

Hi,

 

if you use simple wrap command in vmd, it wraps !ATOMS! around the pbc not WATERS. That means vmd does for example only wrap one H when it crosses the periodic boundaries, the other H and the O will stay on the other side of the box until they cross the boundaries too. This is usually no problem but is not really usable for creating a new start structure. To avoid that, you can use the wrap command with “–compound res” option. This makes that vmd wrap only whole residues. Although this will create a box with waters that are a little out of the boundaries, because not all atoms crossed the pbc, but they get internally wrapped by namd immediately when the simulation starts and should NOT affect the simulation, not so the wrapping of single atoms which produces long bonds that lead to unstable simulations.

 

Good luck.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Hasan haska
Gesendet: Mittwoch, 14. Dezember 2011 13:41
An: Axel Kohlmeyer; namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: cell size

 

Dear Axel,

Thanks for your help. I used “pbc wrap –all” command in VMD and got the coordinates of all water molecules in defined cell sizes ( 40 40 65 ). Then again I used these coordinates to run another md to see if I can transfer wrapped molecule coordinates into another md system and continue md simulation. But, when I run md which starts with a short minimization with wrapped water molecule coordinates I saw the error in below. How can I solve this problem?

 

I want to run md simulations for Liquid/Liquid Interfaces. So First I should equilibrate the water molecules and combine water molecules with a different type of equilibrated molecules to genetate a Liquid/Liquid Interface system then run md for the Liquid/Liquid Interface system. I especially searched for some tutorials or sources for generating Liquid/Liquid Interface system with NAMD and VMD but I coludn’t find anything. Could you please help me about generating the interface system ?

 

 

TCL: Minimizing for 1000 steps

Warning: Low global exclusion count, possible error!

Warning: This warning is not unusual during minimization.

Warning: Increasing pairlistdist or cutoff may avoid this.

PRESSURE: 0 -4418.82 -2.05598 156.051 -2.05598 -4901.6 42486.6 156.051 42486.6 -5.53326e+07

GPRESSURE: 0 -6732.9 704.952 287.812 -1872.49 -5514.03 40747.7 -22321.4 23202.3 -5.33443e+07

ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

 

ENERGY: 0 125379181.5818 4446.9155 0.0000 0.0000 -49473.7045 8194.2763 0.0000 0.0000 0.0000 125342349.0692 0.0000 125342349.0692 125342349.0692 0.0000 -18447311.4967 -17785523.1787 320000.0000 -18447311.4967 -17785523.1787

 

OPENING EXTENDED SYSTEM TRAJECTORY FILE

MINIMIZER SLOWLY MOVING 115 ATOMS WITH BAD CONTACTS DOWNHILL

Warning: Low global exclusion count, possible error!

Warning: This warning is not unusual during minimization.

Warning: Increasing pairlistdist or cutoff may avoid this.

PRESSURE: 1 -4374.24 -3.04685 157.66 -3.04685 -4855.75 42482.4 157.66 42482.4 -5.53325e+07

GPRESSURE: 1 -6676.79 671.979 302.936 -1858.45 -5466.59 40737.3 -22320.5 23195 -5.33442e+07

ENERGY: 1 125379181.5818 4446.9155 0.0000 0.0000 -49550.7012 8257.6139 0.0000 0.0000 0.0000 125342335.4100 0.0000 125342335.4100 125342335.4100 0.0000 -18447252.8218 -17785457.4470 320000.0000 -18447252.8218 -17785457.4470

 

..

 

 

  _____

From: Axel Kohlmeyer <akohlmey_at_gmail.com>
To: Hasan haska <hasanhaska_at_yahoo.com>
Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Sent: Tuesday, December 13, 2011 6:00 PM
Subject: Re: namd-l: cell size

On Tue, Dec 13, 2011 at 10:47 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:
>
> ________________________________
> From: Hasan haska <hasanhaska_at_yahoo.com>
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Sent: Tuesday, December 13, 2011 5:46 PM
>
> Subject: Re: namd-l: cell size
>
> Dear Axel,
>
> I modified the conf file like in below and run a short md but I still got
> the some water molecules' coordinates outside the box. I think this is
> normal since I use PBC. Is there any other way to get the coordinates in a
> periodic box ( 40 40 65 ) ?

have you tried using wrapAll ?
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node33.html

other than that, wrapping of coordinates
can easily done in post-processing, e.g.
using the pbctools plugin in VMD.

axel.

>
> Thanks for your help.
>
> useGroupPressure no
> useFlexibleCell no
> useConstantArea no
>
> ________________________________
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: Hasan haska <hasanhaska_at_yahoo.com>
> Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Sent: Tuesday, December 13, 2011 4:21 PM
> Subject: Re: namd-l: cell size
>
> On Tue, Dec 13, 2011 at 9:10 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:
>> Dear Namd Users,
>>
>> I run 5 ns md simulation for water molecules with the conf file below. And
>> I
>> want to get the final coordinates of all water molecules in defined cell
>> sizes ( 40 40 65 ) . How can I do this operation in NAMD ?
>
> don't use a flexible cell?
>
> axel.
>
>>
>> Thank you very much for your help.
>>
>> Regards.
>>
>> *********
>> #--- This is a test namd configuration file
>>
>> paratypeCharmm on
>> parameters water.prm
>>
>> structure water.psf
>> coordinates water.pdb
>> outputName water_1out
>>
>> set temperature 300
>> temperature $temperature
>>
>>
>> firsttimestep 0
>>
>> # Integrator Parameters
>> timestep 1
>> nonbondedFreq 1
>> fullElectFrequency 5
>> stepspercycle 10
>>
>>
>>
>>
>> # Force-Field Parameters
>> exclude scaled1-4
>> 1-4scaling 0.8333333
>> cutoff 19.7
>> switching on
>> switchdist 17
>> pairlistdist 24
>>
>>
>>
>> # Constant Temperature Control
>> langevin on ;# do langevin dynamics
>> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
>> langevinTemp $temperature
>> langevinHydrogen on ;# don't couple langevin bath to hydrogens
>>
>>
>> #--- PBC
>>
>>
>> cellBasisVector1 40. 0.0 0.0
>> cellBasisVector2 0.0 40. 0.0
>> cellBasisVector3 0.0 0.0 65.
>>
>> #--- PME
>>
>> dielectric 1
>> PME on
>> PMEGridSizeX 45
>> PMEGridSizeY 45
>> PMEGridSizeZ 72
>>
>> # Constant Preswaterre Control (variable volume)
>> useGroupPressure no
>> useFlexibleCell yes
>> useConstantArea yes
>>
>> langevinPiston on
>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> langevinPistonPeriod 200.
>> langevinPistonDecay 100.
>> langevinPistonTemp $temperature
>>
>>
>> #--- Output & Restart
>>
>> binaryoutput no
>>
>> binaryrestart yes
>>
>> restartname water_restart
>> DCDfile water_out.dcd
>>
>>
>> restartfreq 1250
>> dcdfreq 1250
>> xstFreq 1250
>> outputEnergies 1250
>> forceDCDfreq 1250
>> outputPressure 1250
>> outputtiming 1250
>>
>> minimize 12500
>> reinitvels $temperature
>>
>> run 5000000
>>
>> *************
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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