Thanks!
2014-08-20 14:05 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com:
Hi,
You should be using a supported host compiler for your version of CUDA
(check its docs, probably gcc 4.7 or 4.8, for example), rather than clang.
Mark
On Wed, Aug 20, 2014 at 9:59 AM, Valentina Loconte
at gpu_utils_generated_memtestG80_core.cu.o.cmake:206 (message):
Error generating
/Users/Valentina/Software/gromacs-4.6.6/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o
make[2]: ***
[src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_memtestG80_core.cu.o]
Error
Thank you, this makes perfect sense!
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Hi,
As Vitaly said, you are mixing the methods.
If you want to find out the potential between 2 atoms, why don't you just go
into the FF, pick out relevant parameters from there and plot it. So for 2
non-bonded atoms the contribution would be VdW and Coulomb.
Putting things further than
Hi,
You need to make index containing all the angles you want to calculate the
angle for. You could just manually edit the .ndx by combining all entries
under one header, i.e. deleting all headers but first.
Hope it helps,
V
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Thank you Justin.
This is what I have tried, but obviously gone wrong with [settles]. I'll try
again.
V
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Hello,
I need an advise on how it is better to approach the ThermoD integration of
such system:
+vely charged inorganic layer, filled with water and counterbalanced by -ve
organics
Do I integrate out organics both VdW and Coulomb, making the system have
total +ve charge at lambda = 1
OR:
Do I
Thank you for your reply. I am now suspecting charges to be a problem.
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I still cannot resolve this problem. Is there any way to find out what is
causing Segmentation Fault? Normally Gromacs provides quite comprehendible
errors, but this one.
I have checked the charges against DFT.
I also have the output of the system simulated with Discover. I am using
that force
potentials.
I would be very happy to hear any advises,
Thank you
V
Full md.log:
valentina$ more md.log
Log file opened on Tue Nov 26 22:07:50 2013
Host: oparin01.earthsci.dur.ac.uk pid: 18263 nodeid: 0 nnodes: 1
Gromacs version:VERSION 4.6
Precision: single
Memory model
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