<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Hi,</div><div><br></div><div>this is the system I was using. I have also done some</div><div>debugging:</div><div>by using -debug 10 flag in mdrun I got this result in mdrun.debug</div><div><br></div><div><br></div><div><br></div><div><div>Increasing GB neighbourlist j size to 3190</div><div>Increasing GB neighbourlist j size to 7986</div><div>Increasing GB neighbourlist j size to 18489</div><div>Increasing GB neighbourlist j size to 41490</div><div>fshift after SR (45x3):</div><div> fshift after SR[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> fshift after SR[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> fshift after SR[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> fshift after SR[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> fshift after ...</div><div><br></div><div> fshift after SR[ 22]={-3.59985e+269, 7.91323e+269, -1.16757e+270}</div><div> and all the other 0.00</div><div><br></div><div><div>vir_part (3x3):</div><div> vir_part[ 0]={1.52302e+270, 6.71165e+268, -9.94015e+268}</div><div> vir_part[ 1]={6.71165e+268, 1.38159e+270, -5.32724e+267}</div><div> vir_part[ 2]={-9.94015e+268, -5.32724e+267, 1.03656e+270}</div><div>Guessed pbc = xyz from the box matrix</div><div>Guessed pbc = xyz from the box matrix</div><div>constraint virial (3x3):</div><div> constraint virial[ 0]={-1.06645e+269, -6.31248e+267, 5.52275e+267}</div><div> constraint virial[ 1]={-6.31248e+267, -1.16995e+269, -5.31208e+267}</div><div> constraint virial[ 2]={5.52275e+267, -5.31208e+267, -1.01260e+269}</div><div>dekin (3x3):</div><div> dekin[ 0]={ -inf, -inf, inf}</div><div> dekin[ 1]={ -inf, -inf, inf}</div><div> dekin[ 2]={ inf, inf, -inf}</div><div> ekin (3x3):</div><div> ekin[ 0]={ 1.07090e+02, -1.28235e+01, 2.44544e+00}</div><div> ekin[ 1]={-1.28235e+01, 9.93836e+01, -4.73968e+00}</div><div> ekin[ 2]={ 2.44544e+00, -4.73968e+00, 8.31171e+01}</div><div>dekin = -inf, ekin = 289.591 vcm = (37724423208582392295386276764510319211320417140435671882380328320812381594880211169413371</div><div>358679334568178120349284174636383420665585500528416721787062413484436933391583994571739322882089364956909490686430616721178287</div><div>5654860436192621173254981676957696.0000 31180390611175245501077433199741281911130739631997505115600164449706783479065192251777</div><div>314796409899660965811414664650242000195439480951995994394538761200379988057180467500001038548378320832492673848303062076640322</div><div>1353454826879291876975370559962480640.0000 -1431266541249085767742382230423258785149802680554631655691802070662038285164031728</div><div>191772385960655935292355927541486927054477721966709871891976853820786315670152588754868888831140838914572678663771823871985711</div><div>373255227035928103075818815545438543806464.0000)</div><div><br></div><div><br></div><div><br></div><div><br></div><div>moreover after having take a look at the code in genborn.c it seems to me that fr->invsqrta in not properly initialized before the first step.</div><div><br></div><div>hope this helps,</div><div>Regards,</div><div>Carlo</div></div><div><br></div><div><div>On 1 Jun 2010, at 12:58, Per Larsson wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi!<div><br></div><div>Could you send me your inputfiles, and I'll have a look at it.</div><div>It should work.</div><div><br></div><div>Regards</div><div>/Per</div><div><br></div><div><br><div><div>1 jun 2010 kl. 12.30 skrev Pär Bjelkmar:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Sett detta?<br><div><br><div>Vidarebefordrat brev:</div><br class="Apple-interchange-newline"><blockquote type="cite">Message: 1<br>Date: Tue, 1 Jun 2010 11:35:13 +0200<br>From: Carlo Camilloni <<a href="mailto:carlo.camilloni@gmail.com">carlo.camilloni@gmail.com</a>><br>Subject: [gmx-developers] implicit solvent in the git version of<br><span class="Apple-tab-span" style="white-space: pre; "> </span>gromacs<br>To:<span class="Apple-converted-space"> </span><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>Message-ID: <<a href="mailto:64B168DC-C53F-406B-BA7B-091B3F243527@gmail.com">64B168DC-C53F-406B-BA7B-091B3F243527@gmail.com</a>><br>Content-Type: text/plain; charset=us-ascii<br><br>Dear Gromacs Developers,<br><br>I am trying to test, without any success, the implicit solvent algorithm implemented in the git version of gromacs.<br>I am using a 16 residue beta-hairpin with the charmm forcefield and all the different implicit algorithm still, ecc.<br>But the system explode within the first steps, while turning-off the gbsa all goes well.<br><br>pbc=no<br>electrostatic=reaction-field-zero or cut-off<br>vdw=shift or cut-off<br>dt=0.002 or 0.001<br>constraint=lincs<br>nstlist=1<br>rlist=rgblist=2<br>both with temperature coupling as without.<br><br>Is the algorithm still broken?<br><br>Best regards,<br>Carlo Camilloni</blockquote></div><br></div></blockquote></div><br></div></div></blockquote></div><br></div></div></blockquote></div><br></div></body></html>