Hi,<div><br></div><div>The dhfr benchmark files were prepared for the OpenMM-accelerated mdrun (called mdrun-gpu in 4.5 and renamed to mdrun-openmm in 4.6 to avoid confusion with the native GPU acceleration).</div><div><br>
</div><div>However, the native GPU acceleration does not support implicit solvent simulation, for those purposes you should build mdrun-openmm (GMX_GPU=ON in CMake).</div><div><br></div><div>You you preferably use the 4.6 code-base (release-4-6 branch) which is more stable than the 5.0 code-base (master branch) that you are trying to use.</div>
<div><br></div><div>Cheers,</div><div class="gmail_extra"><br clear="all">--<br>Szilárd<br>
<br><br><div class="gmail_quote">On Fri, Nov 16, 2012 at 10:42 PM, Thomas Evangelidis <span dir="ltr"><<a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear GROMACS developers,<br><br>I am confused about the supporting features of GROMACS-GPU VERSION 5.0-dev-20121027-d2934a9-dirty regarding implicit solvent simulations. I have downloaded the benchmark set from <a href="http://www.gromacs.org/Documentation/Installation_Instructions/GPUs#Benchmark_systems" target="_blank">http://www.gromacs.org/Documentation/Installation_Instructions/GPUs#Benchmark_systems</a> but cannot run the GPU/dhfr-impl-1nm.bench, GPU/dhfr-impl-2nm.bench and GPU/dhfr-impl-inf.bench cases. I.e. with the dhfr-impl-1nm.bench I get:<br>
<br>mdrun_intel_cuda5 -v -s topol.tpr -debug 1<br><br>NOTE: GPU(s) found, but the current simulation can not use GPUs<br> To use a GPU, set the mdp option: cutoff-scheme = Verlet<br> (for quick performance testing you can use the -testverlet option)<br>
<br><br>but -testverlet yields:<br><br>mdrun_intel_cuda5 -v -s topol.tpr -debug 1 -testverlet<br><br>Fatal error:<br>Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc<br><br clear="all">Were these benchmarks made for the older versions of GROMACS-GPU that implemented OpenMM? Otherwise how can I run them as they are now?<br>
<br>thanks in advance,<br>Thomas <br>
<br><br><br><br>
<br>--<br>
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