From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Jan 02 2014 - 09:53:35 CST
Another possible error might be that your membrane is not equilibrated -it
is not obvious in your script whether you did it before the step that
fails. Typically, in protein-membrane systems we follow several stages of
equilibration. The following is an outline of the stages I follow with the
lipid11 force field that requires constant surface tension (NPgT ensemble):
# Stage 1: minimization of lipid tails only, the rest are kept fixed.
# Stage 2: minimization of the whole system apart from the protein which is
constrained to its initial configuration. Then the system is slowly heated
up to 320 K and
# a small equilibration at the NPgT ensemble of 0.5 ns is
conducted with the protein constrained.
# Stage 3: NPgT equilibration with no constraints.
In your case (CHARMM ff) the surface tension is not necessary. Also the
final temperature depends of the lipid constitution of the membrane. Have a
look at the NAMD protein-membrane tutorial for more info...
On 2 January 2014 02:17, PANAGIOTA KYRIAKOU <kyria008_at_gmail.com> wrote:
> Hi there,
> Thanks for your answer..
> I thought the use of the commands reassignFreq, reassignTemp etc was
> gradual heating. I just do not understand what I am doing wrong.
> I had problems with the constrains so this is why I used 1fs.
>
> Giota
>
>
>
> Panagiota Kyriakou
>
> Graduate Student
>
> Dept. of Chemical Engineering and Materials Science
>
> University of Minnesota
>
>
> email: kyria008_at_umn.edu
>
>
> On Wed, Jan 1, 2014 at 9:27 AM, Thomas Evangelidis <tevang3_at_gmail.com>wrote:
>
>> Energy minimization is like dropping the temperature of the system to 0
>> Kelvin. Therefore, in order to initialize velocities at 303 Kelvin you must
>> first do the gradual heating from 0->303 K otherwise the system will blow
>> up. Unlike GROMACS or AMBER, NAMD does not do the heating automatically.
>> Replace "run 1000000" with something like:
>>
>> # Heating
>> set HeatSteps 5
>> set HeatMDsteps 1000
>> for {set i 1} {$i <= $HeatSteps } { incr i } {
>> set t [expr $temp*$i/$HeatSteps]; puts "Heat structure to $t K
>> for $HeatMDsteps steps."
>> reinitvels $t
>> run $HeatMDsteps
>> }
>> reinitvels $temp
>> run 1000000 ;# 1 ns at $temp Kelvin
>>
>>
>> Also are you sure you want to use a timestep of 1 fs?
>>
>>
>> On 31 December 2013 19:28, PANAGIOTA KYRIAKOU <kyria008_at_gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I have been trying to equilibrate my system that consists of protein
>>> embedded in a membrane and I get the following error:
>>>
>>> *TIMING: 500000 CPU: 9750.65, 0.021551/step Wall: 9750.65,
>>> 0.021551/step, 0 hours remaining, 556.101562 MB of memory in use.*
>>> *ETITLE: TS BOND ANGLE
>>> DIHED IMPRP ELECT VDW
>>> BOUNDARY MISC KINETIC TOTAL TEMP
>>> POTENTIAL TOTAL3 TEMPAVG PRESSURE
>>> GPRESSURE VOLUME PRESSAVG GPRESSAVG*
>>> *ENERGY: 500000 48376.8664 114689
>>> <8664%20%C2%A0%20%C2%A0114689>.7899 11643.7243 506.4399
>>> -580965.4098 103191 <4098%20%C2%A0%20%C2%A0103191>.7767 0.0000
>>> 246.2954 0.0000 -302310.5171 0.0000
>>> -302310.5171 -302310.5171 0.0000 6488.4885
>>> 6928.4046 1914140.8650 6488.4885 6928.4046*
>>>
>>> *WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500000*
>>> *WRITING COORDINATES TO DCD FILE AT STEP 500000*
>>> *WRITING COORDINATES TO RESTART FILE AT STEP 500000*
>>> *FINISHED WRITING RESTART COORDINATES*
>>> *WRITING VELOCITIES TO RESTART FILE AT STEP 500000*
>>> *FINISHED WRITING RESTART VELOCITIES*
>>> *TCL: Writing to files with basename A_equil_1_min.*
>>> *WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500000*
>>> *WRITING COORDINATES TO OUTPUT FILE AT STEP 500000*
>>> *WRITING VELOCITIES TO OUTPUT FILE AT STEP 500000*
>>> *TCL: Running for 1000000 steps*
>>> *REASSIGNING VELOCITIES AT STEP 500000 TO 303.15 KELVIN.*
>>> *colvars: Writing the state file "A_equil_1.restart.colvars.state".*
>>> *colvars: Synchronizing (emptying the buffer of) trajectory file
>>> "A_equil_1.colvars.traj".*
>>> *ERROR: Constraint failure in RATTLE algorithm for atom 6522!*
>>> *ERROR: Constraint failure; simulation has become unstable.*
>>> *ERROR: Constraint failure in RATTLE algorithm for atom 13834!*
>>> *ERROR: Constraint failure; simulation has become unstable.*
>>> *ERROR: Constraint failure in RATTLE algorithm for atom 1812!*
>>> *ERROR: Constraint failure; simulation has become unstable.*
>>>
>>> When I tried to fix it I realized that the Temperature increased from 0
>>> to 312 K, instantly after minimization even though I am using temperature
>>> reassignment. Here is my configuration file:
>>>
>>>
>>> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
>>> *# Custom variables*
>>> *set temp 303.15 *
>>>
>>> *# inputs*
>>> * structure ../A.psf ; *
>>> * coordinates ../A.pdb ;*
>>> * paraTypeCharmm on*
>>> * parameters ../../common/topology/par_all36_prot_nomass.prm*
>>> * parameters ../../common/topology/par_all36_water_ions.prm *
>>> * parameters ../../common/topology/par_all36_lipid.prm *
>>>
>>>
>>> * temperature $temp ;*
>>> * # simulation parameters*
>>> * outputname A_equil_1 ;*
>>> * outputEnergies 1000 ;*
>>> * outputTiming 1000 ;*
>>> * xstFreq 10000 ;*
>>> * dcdFreq 10000 ;*
>>> * dcdUnitCell yes *
>>> * binaryoutput on ;*
>>> * restartfreq 10000 ;*
>>> * seed 1369948321 ;*
>>>
>>> *# calculation parameters*
>>> * exclude scaled1-4 ;*
>>> * 1-4scaling 1.0 ;*
>>> * switching on ;*
>>> * switchDist 9 ;*
>>> * cutoff 10 ;*
>>> * pairlistdist 12 ; *
>>> * stepsPerCycle 20 ;*
>>> * rigidbonds all ;*
>>> * vdwForceSwitching yes ;*
>>> * timestep 1 ; *
>>> * nonBondedFreq 1 ;*
>>> * fullElectFrequency 1 ;*
>>> * cellBasisVector1 139.65999603271484 00.00 00.00 ;*
>>> * cellBasisVector2 00.00 140.35699462890625 00.00 ;*
>>> * cellBasisVector3 00.00 00.00 97.64900207519531 ;*
>>> * cellorigin -0.9953396916389465 4.457383155822754
>>> 2.071026086807251 ;*
>>> * wrapAll on ;*
>>> * wrapWater on ;*
>>> * wrapNearest off ;*
>>>
>>> *# PME*
>>> * Pme on ;*
>>> * PmeGridsizeX 144 ;*
>>> * PmeGridsizeY 150 ;*
>>> * PmeGridsizeZ 108 ;*
>>>
>>>
>>> *# Control (need to be specified before runs) *
>>> * useFlexibleCell yes ;*
>>> * useGroupPressure yes ;*
>>> * useConstantRatio yes ;*
>>>
>>> *# constant pressure*
>>> * langevinPiston on*
>>> * langevinPistonTarget 1.01325*
>>> * langevinPistonPeriod 50.0*
>>> * langevinPistonDecay 25.0*
>>> * langevinPistonTemp $temp*
>>>
>>> * reassignFreq 1000 ;*
>>> * reassignTemp 1 ;*
>>> * reassignIncr 1 ;*
>>> * reassignHold $temp ; *
>>>
>>> * colvars on*
>>> * colvarsConfig ../restraints/A_equil_1.col *
>>>
>>>
>>> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
>>> * # EXECUTION*
>>>
>>> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
>>> * minimize 500000*
>>>
>>> * run 1000000*
>>>
>>>
>>> Do you know what could have caused the increase in the temperature?
>>> I would appreciate your help so much,
>>>
>>> Giota
>>>
>>> Panagiota Kyriakou
>>>
>>> Graduate Student
>>>
>>> Dept. of Chemical Engineering and Materials Science
>>>
>>> University of Minnesota
>>>
>>>
>>> email: kyria008_at_umn.edu
>>>
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: tevang_at_pharm.uoa.gr
>>
>> tevang3_at_gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:23 CST