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

n 6, 2013 at 4:38 AM, Sikandar Mashayak wrote: > 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.

[gmx-users] Full Hessian matrix in readable format

y, my searches in the manual (gmxdump, g_nmeig) and in the list archives didn't result in anything other than the eigenvalues and the displacement vectors of the normal modes. Any hints? Thanks! -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto

Re: [gmx-users] Minimization problem

tepsize. The warning you mentioned 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 Sã

Re: [gmx-users] Minimization problem

_cg.edr > Found: step=-1, nre=36, nblock=0, time=-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 3

Re: [gmx-users] Bonded parametrs for CG

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 Materiai

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

der Spoel Force Field Benchmark of Organic Liquids: Density, 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 30

Re: [gmx-users] when?

sic_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 maili

Re: [gmx-users] qyestion about restriction

eezedim 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 listgmx-user

Re: [gmx-users] mdrun graceful exit

ficantly > 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 Instit

Re: [gmx-users] Re:Shell scripts

placing the here-document by a here-string, but that's 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

[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 list

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

On Fri, Jun 15, 2012 at 5:46 PM, Shima Arasteh 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.: +55 11 3091-

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

On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar 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 Tel

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

en ends? If you can 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

Re: [gmx-users] pdb2gmx angles and dihedrals

rsion and followed some of the discussion on Gerrit. I'll submit my suggestions to the redmine site to avoid 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

Re: [gmx-users] pdb2gmx angles and dihedrals

yone clarify the role of these extra columns? I think this >> also hints for a review in this section of the manual. > > > True. An update 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! ;) Gr

[gmx-users] pdb2gmx angles and dihedrals

t 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! -- Elto

Re: [gmx-users] Velocity autocorrelation function

On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal wrote: > Using g_velacc I can calculate the velocity autocorrelation function of a > group as a vector. > > Can I calculate the velocity autocorrelation function as a scalar? My naïve suggestion would be to take the norm of that vector

Re: [gmx-users] Constraints and efficency

On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham 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 simulatio

[gmx-users] Constraints and efficency

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 F

Re: [gmx-users] Re Multiple Chains

to adjust 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 list

Re: [gmx-users] How to select atoms dynamically

Zhongjin He Hello, zhongjin. May I contact you off-list with some questions about CNT in GROMACS? -- 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] abnormal stop of job

ackground. > Thanks > Atanu > > > ____ > From: Elton Carvalho > To: Discussion list for GROMACS users > 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

Re: [gmx-users] abnormal stop of job

On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal 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. -- El

Re: [gmx-users] frezzing a bond

tation time 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-u

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

On Tue, Jul 13, 2010 at 10:52 PM, Mark Abraham 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 >

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

On Mon, Jul 12, 2010 at 9:29 PM, Mark Abraham 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", >> &g

[gmx-users] Compile-time errors with MKL

quot; 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 Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Fí

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

n adding opls energies 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 - 0