Dear Ross and Callum
Thanks a lot for inputs and details
P.S.: (yahoo mail is creating problem somehow not keeping previous mail in track, 'sorry to future searches')
On Friday, January 31, 2014 5:13 PM, "Dickson, Callum J" <callum.dickson09.imperial.ac.uk> wrote:
Hi Jio,
Actually in the inputs I used are I think the same or similar to what I posted a while ago but here they are again (temperature is at 303K), plus the script I use to run a lipid simulation on a GPU:
-----Minimization [01_Min.in]:
minimize
&cntrl
imin=1,maxcyc=10000,ncyc=5000,
ntb=1,ntp=0,
ntf=1,ntc=1,
ntpr=50,
ntwr=2000,
cut=10.0,
/
-----Heat NVT [02_Heat.in]:
heating LIPID 128 100K
&cntrl
imin=0, ntx=1, irest=0,
ntc=2, ntf=2, tol=0.0000001,
nstlim=2500, ntt=3, gamma_ln=1.0,
ntr=1, ig=-1,
ntpr=100, ntwr=10000,ntwx=100,
dt=0.002,nmropt=1,
ntb=1,ntp=0,cut=10.0,ioutfm=1,
/
&wt type='TEMP0', istep1=0, istep2=2500,
value1=0.0, value2=100.0 /
&wt type='END' /
Hold lipid fixed
10.0
RES 1 384
END
END
-----Equilibrate NPT [03_Heat2.in]:
heating LIPID 128 303K
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2,tol=0.0000001,
nstlim=50000, ntt=3, gamma_ln=1.0,
ntr=1, ig=-1,
ntpr=100, ntwr=10000,ntwx=100,
dt=0.002,nmropt=1,
ntb=2,ntp=2,taup=2.0,cut=10.0,ioutfm=1,ntxo=2,
/
&wt type='TEMP0', istep1=0, istep2=50000,
value1=100.0, value2=303.0 /
&wt type='END' /
Hold lipid fixed
10.0
RES 1 384
END
END
----10x 500ps with this input to allow box to relax (the restarts are required to overcome the skinnb error) [04_Hold.in]:
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=250000, ntt=3, gamma_ln=1.0,
temp0=303.0,
ntpr=5000, ntwr=5000, ntwx=5000,
dt=0.002, ig=-1,
ntb=2, ntp=2, cut=10.0, ioutfm=1,ntxo=2,
/
/
&ewald
skinnb=5,
/
-----Production run NPT 303K for 125ns [05_Prod.in]:
pro 125ns LIPID 303K
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=62500000, ntt=3, gamma_ln=1.0,
temp0=303.0,
ntpr=5000, ntwr=500000, ntwx=5000,
dt=0.002, ig=-1,
ntb=2, ntp=2, cut=10.0, ioutfm=1,ntxo=2,
/
-----bash script to perform a GPU lipid run:
#!/bin/bash
export CUDA_VISIBLE_DEVICES="0"
lipid=DMPC_128
prmtop=$lipid.prmtop
## Equilibration ##
/usr/local/bin/pmemd.cuda_SPFP -O -i 02_Heat.in -o 02_Heat.out -p $prmtop -c 01_Min.rst -r 02_Heat.rst -x 02_Heat.nc -ref 01_Min.rst
/usr/local/bin/pmemd.cuda_SPFP -O -i 03_Heat2.in -o 03_Heat2.out -p $prmtop -c 02_Heat.rst -r 03_Heat2.rst -x 03_Heat2.nc -ref 02_Heat.rst
cp 03_Heat2.rst hold_0.rst
# 10 x 500ps NPT runs to collapse box and avoid skinnb error ##
for i in $(seq 1 1 10)
do
k=$(($i - 1))
/usr/local/bin/pmemd.cuda_SPFP -O -i 04_Hold.in -o hold_$i.out -p $prmtop -c hold_$k.rst -r hold_$i.rst -x hold_$i.nc
done
## Main run ##
/usr/local/bin/pmemd.cuda_SPFP -O -i 05_Prod.in -o 05_Prod_$lipid.out -p $prmtop -c hold_10.rst -r 05_Prod_$lipid.rst -x 05_Prod_$lipid.nc -inf 05_Prod_$lipid.mdinfo
All the best,
Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Jio M [jiomm.yahoo.com]
Sent: 31 January 2014 15:11
To: AMBER Mailing List
Subject: Re: [AMBER] status of the Amber lipid framework?
hi
Its out of date indeed. I think all future publications should include not only AMBER version but the latest applied patches information as well ;)
this discussion gone somewhat out of topic I think, just a humble gentle reminder about Lipid 14 inputs; if possible.
thanks
On Friday, January 31, 2014 2:57 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Fri, 2014-01-31 at 06:43 -0800, Jio M wrote:
> Hi Jason
>
> Thanks, I can run this on my machine and I installed it recently:
> $AMBERHOME/update_amber --version
>
> But this update_amber does not exist (in $AMBERHOME) in installed AMBER version (some central facility). Is there some other way? I can see though it was installed somewhat in June 2012! and I think update_amber is new? Also not sure which bug fixes they have applied.
If update_amber does not exist then it is very out-of-date.
update_amber replaces patch_amber.py. You can go to $AMBERHOME and run
the command "./patch_amber.py --patch-level" to get the same
information, but the fact that update_amber is not present gives you
your answer ;).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 31 2014 - 10:00:02 PST
