From: arpita agarwal (arpita284_at_gmail.com)
Date: Fri Apr 22 2016 - 02:54:50 CDT
Hi Arash,
Thank you for your reply.
I have assigned those values as per my protein. While sending it to the
mailing list, I had just replaced them with variables. Sorry for this.
Could you tell me about these example files where periodic boundary
simulations have been used as I have not come across any of them.
I need any reference where replica exchange has been done using NAMD with
periodic boundary conditions. When I am running this without PBC, I am not
facing any problems.
Thank you.
Regards,
Arpita
On Fri, Apr 22, 2016 at 4:39 PM, Arash Azari <arashazari.temp_at_gmail.com>
wrote:
> Hi Arpita,
>
> I am sure that you have received some responses so far, just in case you
> have not. Where did you assigned the values for the x,y,z, a,b,c, x1,y1,z1?
> you should measure the x,y,z and a,b,c and put them explicitly into the
> input file, or measure them by TCL script inside the input file. Please
> look at the user manual and the example files.
> That is why the non-periodic simulation works and the PBC fails.
> HTH,
>
>
> Best regards,
> Arash
>
>
> On Thu, Apr 21, 2016 at 7:43 AM, arpita agarwal <arpita284_at_gmail.com>
> wrote:
>
>> Dear All,
>>
>> I am trying to run replica exchange for a protein with 8 replicas. Below
>> is my configuration file:-
>>
>> timestep 1.0
>>
>> structure protein.psf
>> coordinates protein.pdb
>>
>> margin 5.0
>>
>> stepspercycle 10
>> paratypecharmm on
>> parameters par_all27_prot_lipid.prm
>>
>> exclude scaled1-4
>> 1-4scaling 1.0
>> switching on
>> switchdist 10.0
>> cutoff 12.
>> pairlistdist 14.
>>
>> langevin on
>> langevinDamping 5.0
>> langevinHydrogen off
>>
>> rigidBonds all
>> nonbondedFreq 1
>> fullElectFrequency 2
>>
>> wrapAll on
>> wrapWater on
>> wrapNearest on
>>
>> dcdUnitCell yes
>>
>> useGroupPressure yes
>> useFlexibleCell no
>> useConstantArea no
>> useConstantRatio no
>>
>> langevinPiston no
>> #langevinPistonTarget 1.01325
>> #langevinPistonPeriod 100.0
>> #langevinPistonDecay 50.0
>>
>> #xstFreq 100
>> #outputEnergies 100
>> #outputPressure 100
>>
>> if {1} {
>> cellBasisVector1 x 0.0 0.0 ;# x-value for box
>> dimension
>> cellBasisVector2 0.0 y 0.0 ;# y-value for box
>> dimension
>> cellBasisVector3 0.0 0.0 z ;# z-value for box
>> dimension
>> cellOrigin a b c
>>
>> PME yes
>> PMEGridSizeX x1
>> PMEGridSizeY x2
>> PMEGridSizeZ x3
>> PMEGridSpacing 1.0
>> }
>>
>>
>> When I am running this with periodic boundary conditions(PBC) then I am
>> getting the below error:-
>>
>>
>>
>>
>>
>> *------- Partition 3 Processor 1 Exiting: Caught Signal ------Reason:
>> segmentation violationSuggestion: Try running with '++debug', or linking
>> with '-memory paranoid' (memory paranoid requires '+netpoll' at
>> runtime).Fatal error on Partition 3 PE 1> segmentation violation*
>> I think this is related to memory but there is no such issue being
>> observed.
>>
>> When I am running the same configuration file without PBC, it's running
>> fine.
>>
>> I am using the latest NAMD - NAMD_2.11_Linux-x86_64-netlrts.
>>
>> Kindly suggest what could be the problem here.
>>
>> Thank you.
>>
>> Regards,
>> Arpita Srivastava
>>
>>
>
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