Update:
A little ordering fixes everything! Both the harmonic restraints and distance restraints are being read and applied according to the out.file
NVT prod
&cntrl
irest=1, ntx =5,
nstlim=5000000, dt=0.002,
ntpr=500, ntwr=500, ntwx=500,
temp0=300.0,
ntt=3, gamma_ln=5, ntb=1, ntp=0,
ntc=2, ntf=2, ig=-1,
cut=9,
ioutfm = 1,
iwrap=1, nmropt=1,
ntr=1,
/
&wt type='END' /
DISANG=rst.dist
&end
Hold lipid fixed
10.0
RES 1 384
END
END
However now I'm encountering a new CUDA related problem:
Error: an illegal memory access was encountered launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
Is it possible for one of the CUDA developers to provide insight into this?
Best,
Parker
________________________________________
From: Parker de Waal [Parker.deWaal.vai.org]
Sent: Thursday, September 25, 2014 9:43 PM
To: amber.ambermd.org
Subject: [AMBER] Combined cartesian and NMR restraints
Hello Everyone,
After reading through some of the old mailing list threads regarding the various workarounds for ntr =1 and nmropt=1, I still need some clarification.
I have an NVT prod.in as show below:
NVT prod
&cntrl
irest=1, ntx =5,
nstlim=5000000, dt=0.002,
ntpr=500, ntwr=500, ntwx=500,
temp0=300.0,
ntt=3, gamma_ln=5, ntb=1, ntp=0,
ntc=2, ntf=2, ig=-1,
cut=9,
ioutfm = 1,
iwrap=1, nmropt=1,
ntr=1,
&end
&wt type='END' /
DISANG=rst.dist
Now I wish to add cartesian restraints, following the snippet here: http://ambermd.org/Questions/constraints.html into my rst.dist file as seen below:
# N373 D69 VS
&rst
ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
&end
... (lines removed)
# A150 F244 VS
&rst
ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
&end
Hold GPCR fixed
20.0
RES 1 708
END
END
However whenever I run this the follow error occurs:
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
DISANG=rst.dist
rfree: End of file on unit 5
If someone could provide some input on how to achieve this I would greatly appreciate it.
Best,
Parker
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Received on Thu Sep 25 2014 - 20:00:02 PDT
