Re: [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1
Among other places, there was a thread here two days ago with that title ;-) On Mar 23, 2014 3:34 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: where do you learn this stuff ? ;) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 22 March 2014 21:50 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1 On 3/22/14, 9:13 PM, Collins Nganou wrote: Dear Users, I am unable to generate the file.gro with gromacs.4.6.3-1. However, I have obtained the file.top after using pdb2gmx -f TTb.pdb -o TT.gro -p TT.top -ignh ... This appears after I have change the version of gromacs from 4.5-4 to 4.6.3-1 I am not able to find any error in the output. I will be very grateful the receive any suggestion... I wish you all a blessing weekend Collins My out put : Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 4 residues with 37 atoms chain #res #atoms 1 ' ' 2 37 All occupancies are one Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp Atomtype 1 Reading residue database... (amber99sb-ildn) Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp Residue 109 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp Residue 125 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb Processing chain 1 (37 atoms, 2 residues) Identified residue DT3 as a starting terminus. Identified residue DT4 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 2 residues with 63 atoms Making bonds... Number of bonds was 66, now 66 Generating angles, dihedrals and pairs... Instruction non permise (core dumped) An illegal instruction indicates that the binary was compiled for a different architecture, i.e. an incompatible GMX_CPU_ACCELERATION setting when compiling. Did you copy the binaries over from another machine, or did you compile from source? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Velocity Verlet integrator
Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns out to be non-trivial for the bookkeeping. The easiest way to do this was split the velocity Verlet updates. Also, the additional computational cost of two half steps for velocities is trivial compared to the cost of the forces for almost all systems. On Sun, Mar 23, 2014 at 8:39 AM, Mario Fernández Pendás mariof...@gmail.com wrote: Dear all, In terms of computational efficiency, why the velocity Verlet integrator is implemented in GROMACS in one full step for positions and two half steps for velocities? Would it be more efficient to merge the second halft step for velocities with the first half step of the following scheme, ie, integrating in one full step for velocities? Thank you very much, Mario Fernánez-Pendás -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: illegal instruction (core dumped)
sorry for spamming, but I need to up this thread. I'll delete this after someone answer. Sorry. -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015331.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PME on GPU4.6.2)
Dear list, I have noticed the following changelog from Gromacs 4.6.2: -- Added CUDA PME kernels with analytical Ewald correction Does that mean we can now offload PME computation to GPU? I have not found how... I have noticed two environment variables: GMX_CUDA_NB_ANA_EWALD and GMX_CUDA_NB_TAB_EWALD but even if I export them it does not seem to activate PME on GPU. My technique for verifying is: raise PME accuracy by means of fourierspacing, interpolation etc... and see from the force evaluation time GPU/CPU that the CPU time has increased. Thank you AR -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] False Atommass and charge?
Ok, I found the problem. Compiling a program on my home pc just makes this garbage. Compiling on the cluster is doing fine. I have no idea why it isn't working at home. But at least I know the code itself is correct :) -- View this message in context: http://gromacs.5086.x6.nabble.com/False-Atommass-and-charge-tp5015314p5015335.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PME on GPU4.6.2)
On Sun, Mar 23, 2014 at 6:40 PM, Albert Romano albertm...@aol.com wrote: Dear list, I have noticed the following changelog from Gromacs 4.6.2: -- Added CUDA PME kernels with analytical Ewald correction Does that mean we can now offload PME computation to GPU? No. That refers to short-ranged kernels used with PME. More generally, there'd be little/no advantage in CUDA offload, because it would leave the CPU idle in many cases. In parallel, the CPU-based FFT for PME is latency-bound already, and adding CUDA offload latency would be silly, unless/until GPUs come with on-board network connects, and/or are coupled with really weak CPUs. Mark I have not found how... I have noticed two environment variables: GMX_CUDA_NB_ANA_EWALD and GMX_CUDA_NB_TAB_EWALD but even if I export them it does not seem to activate PME on GPU. My technique for verifying is: raise PME accuracy by means of fourierspacing, interpolation etc... and see from the force evaluation time GPU/CPU that the CPU time has increased. Thank you AR -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: illegal instruction (core dumped)
You got an answer already. Mark On Sun, Mar 23, 2014 at 4:57 PM, ooker ganuongp...@gmail.com wrote: sorry for spamming, but I need to up this thread. I'll delete this after someone answer. Sorry. -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015331.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Add atom to .itp file
I want to create a polarizable particle system consisting of a sphere carying charge q and some size r1 on which a oppositively charge -q is present with some other size r2 . Overall I want to create a colloidal particle . Can anyone please help me in making these sphere (atom ) in itp file ? I want to write some command and I don't know what exactly I have to write . Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Add-atom-to-itp-file-tp5015341.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
