Yes, this SHOULD be done. It is what the Charmm people do. Making the
executive decision to add it into the force fields is above my pay grade.
On 3/25/13 10:32 AM, "Scott Le Grand" <varelse2005.gmail.com> wrote:
>Have you ever thought of giving those hydroxyl's miniscule vdw radii?
>That's how I solved that problem for my Ph.D. thesis where I would
>regularly fall into that trap if I didn't...
>
>
>On Mon, Mar 25, 2013 at 10:22 AM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>> Hi Alessandro,
>>
>>
>> This typically means something is wrong with your structure. What ends
>>up
>> happening is you get a NAN in the force array and then this causes the
>> code to crash when it tries to download things. It is not easy to trap
>>it
>> within the GPU code itself due to the tens of thousands of threads that
>> are running. I would take a careful look at your simulation results -
>>does
>> anything look out of place, are any energies or temperatures
>>unreasonably
>> high, does the structure look ok? One place this is happening seems to
>>be
>> with hydrogen atoms colliding with other atoms - they have zero VDW on
>> hydroxyls and occasionally come too close to other atoms. This was never
>> really a problem in the past since it rare and people didn't run for
>>long
>> but now people are routinely running microsecond+ simulations it is
>> starting to bite more often.
>>
>> Does it always crash in the same place if you start with the same random
>> seed and run the exact same simulation?
>>
>> Have you ever seen it crash if you run on the CPU?
>>
>> If you restart from the previous restart file does it crash very
>>quickly?
>>
>> It's going to take a little digging to figure out what is going wrong
>> unfortunately.
>>
>> All the best
>> Ross
>>
>> On 3/25/13 5:06 AM, "Alessandro Orro" <alessandro.orro.itb.cnr.it>
>>wrote:
>>
>> >dear all
>> >
>> >I'm trying to run a MD simulation with pmemd.cuda using the cmdline
>> >
>> >*time pmemd.cuda -O -i md.in -o md.out -p com.wat.leap.prm7 -c npt.rst7
>> >-ref npt.rst7 -x md.trj -inf md.info -r md.rst7;*
>> >
>> >this is the md.in file
>> >
>> >*production dynamics*
>> >* &cntrl*
>> >* imin=0, irest=1, ntx=5,*
>> >* nstlim=25000000, dt=0.002,*
>> >* ntc=2, ntf=2,*
>> >* cut=10.0, ntb=2, ntp=1, taup=2.0,*
>> >* ntpr=1000, ntwx=1000, ntwr=50000,*
>> >* ntt=3, gamma_ln=2.0,*
>> >* temp0=300.0,*
>> >*/*
>> >
>> >After about 1000 min the run crashes with the error
>> >
>> >*cudaMemcpy GpuBuffer::Download failed unspecified launch failure*
>> >
>> >I also tried with ig=-1 and ntf=1, as suggested by someone in this
>>mailing
>> >list, but the error is the same.
>> >
>> >I think to use the most updated version because the md.out contains
>> >
>> >*|--------------------- INFORMATION ----------------------*
>> >*| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.*
>> >*| Version 12.2*
>> >*| *
>> >*| 01/10/2013*
>> >*| *
>> >*| Implementation by:*
>> >*| Ross C. Walker (SDSC)*
>> >*| Scott Le Grand (nVIDIA)*
>> >*| Duncan Poole (nVIDIA)*
>> >*| *
>> >*| CAUTION: The CUDA code is currently experimental.*
>> >*| You use it at your own risk. Be sure to*
>> >*| check ALL results carefully.*
>> >*| *
>> >*| Precision model in use:*
>> >*| [SPFP] - Mixed Single/Double/Fixed Point Precision.*
>> >*| (Default)*
>> >*| *
>> >*|--------------------------------------------------------*
>> >
>> >using another protein-ligand complex the simulation finished correctly.
>> >Any
>> >suggestions?
>> >
>> >thank you in advance
>> >
>> >Alessandro
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>>
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Received on Mon Mar 25 2013 - 11:00:04 PDT
