Re: [gmx-users] velocity-verlet giving nans

On Thu, Jun 6, 2013 at 4:38 AM, Sikandar Mashayak symasha...@gmail.comwrote: when I run 'mdrun' I am getting 'nan' in output from the first step itself. Does mdrun keep running with NaN after NaN or does it stop with an error message (or segfault for that matter)? Cheers, -- Elton Carvalho Tel

Re: [gmx-users] Minimization problem

=-1. Trying to skip frame expect a crash though* http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica

Re: [gmx-users] Minimization problem

is probably not directly related to mdrun stopping. What's your nstenergy value set in the mdp file? -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing

Re: [gmx-users] Bonded parametrs for CG

the optmized AA structure converted to CG and ad-hoc force constants, and tune them iteratively by comparing the bond length, angle bend and dihedral distributions from the CG simulation with an atomistic trajectory converted to CG. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos

Re: [gmx-users] simmulated annealing excess temperature........................

, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant, J. Chem. Theor. Comput., 8, 61-74 (2012) doi: 10.1021/ct200731v -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica

Re: [gmx-users] when?

/Basic_Git_Usage There you can access the latest versions of the 4.5, 4.6 and master branches. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx

Re: [gmx-users] qyestion about restriction

the freezegrps and freezedim options in the MDP file. See Section 7.3.24 of the manual. Regards, -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing list

Re: [gmx-users] mdrun graceful exit

in significantly better user experience, given most people's workflows. Thanks, Mark. Probably I'll add a feature request in redmine then, since I have no idea how to code such signal handling. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física

[gmx-users] mdrun graceful exit

as if nsteps was reached before convergence and write the relevant gro and trr files? Thanks! -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx

Re: [gmx-users] Re:Shell scripts

personal taste. You may or may not have problems with older versions of bash Greetings from a foggy Groningen, -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users

Re: [gmx-users] protein near the edges of simulation box

On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: You can specify the protein to have no net center of mass motion, by setting it as comm_grps in the .mdp file. If the user is just concerned about visualization, trjconv -center solves his problem. -- Elton Carvalho

Re: [gmx-users] protein near the edges of simulation box

On Fri, Jun 15, 2012 at 5:46 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear Elton, Where am I supposed to use trjconv -center ? when I want to get the mdrun? As Justin mentioned, you should use if after mdrun, on your .xtc (or.trr) files. Check the manual. -- Elton Carvalho Tel

Re: [gmx-users] keep the nanotube cylindrical.

afford to have periodic tubes, so that the box z length is a multiple of the tube unit cell and the tube ends are bonded through the box wall, it seems much more stable. Or you could try capped tubes. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de

Re: [gmx-users] pdb2gmx angles and dihedrals

cluttering the list. Thanks for the help! -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] pdb2gmx angles and dihedrals

is in progress now. That's great news! In the next days I'll send some questions about the manual to help guiding that effort! ;) Greetings from a sunny Groningen, -- Elton Carvalho Faculty of mathematics and natural sciences University of Groningen attachment: PTB.jpg-- gmx-users mailing listgmx

[gmx-users] pdb2gmx angles and dihedrals

with the manual. In particular, Col8 set to 1 seems to remove dihedrals over bonds with any dihedral, not only those defined under the  [ impropers ] directive. Could anyone clarify the role of these extra columns? I think this also hints for a review in this section of the manual. Thanks! -- Elton Carvalho

Re: [gmx-users] Velocity autocorrelation function

of that vector. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Constraints and efficency

On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 5/01/2011 5:53 AM, Elton Carvalho wrote: [...] Does the larger timestep allowed by eliminating high-frequency O-H vibrations outweigh the time needed by SETTLE? Most definitely. Typical GROMACS simulations report

[gmx-users] Constraints and efficency

, but, as implemented, this doesn't seem possible with the code as is. My molecular dynamics background is based on Cerius2, so please pardon some lack of intimacy with GROMACS behaviour. Regards, -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física

Re: [gmx-users] Re Multiple Chains

the starting configuration? Have you tried manipulating the molecules with VMD? -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users

Re: [gmx-users] abnormal stop of job

running background. Thanks Atanu From: Elton Carvalho elto...@if.usp.br To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, August 5, 2010 1:59:39 PM Subject: Re: [gmx-users] abnormal stop of job On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal

Re: [gmx-users] abnormal stop of job

On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal psamra...@yahoo.com wrote: Received the TERM signal, stopping at the next step The TERM signal is the default signal sent by the command kill to stop a job. Pressing Ctrl-C while the program is running on the foreground has the same effect. -- Elton

Re: [gmx-users] frezzing a bond

as if the bonds were free? Is it possible to use constraints in gromacs as I mentioned above? Thanks -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing list

Re: [gmx-users] Compile-time errors with MKL

On Mon, Jul 12, 2010 at 9:29 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/07/10 08:20, Elton Carvalho wrote: and edit line 26576 of ./config to read LIBS=-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core $LIBS instead of LIBS=-lmkl $LIBS, That seems like asking for trouble. Why

Re: [gmx-users] Compile-time errors with MKL

On Tue, Jul 13, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/07/2010 11:28 PM, Elton Carvalho wrote: Because using -lmkl returns an error like -lmkl not found, so, to remove -lmkl from the configure I need to edit the line. That is what earlier posts in this list (which

[gmx-users] Compile-time errors with MKL

setups of CPPFLAGS and LDFLAGS, also with -lmkl in ./configure give mkl not found sort of errors. This one seems to be the setup that got most far. Any ideas to solve this? I have mkl versions 11.1/072 and 10.2.5.035. Linking to each of them gives similar errors. Thanks in advance -- Elton

Re: [gmx-users] Martini + other force field

for it? -- Prevaleço-me do ensejo para reiterar a Vossa Excelência protesto de elevada estima e consideração. Elton Carvalho Tel.: +55 11 3091-6881/6979 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil