Re: [gmx-users] Reducing Standard Error output

Jack Shultz wrote: Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings That is always necessary if you don't want an expensive random number generator. Your simulation system is ill conditioned, and the l

Re: [gmx-users] Grompp failed under double precision

Jack Shultz wrote: We have a workflow going, and I switched to double precision because of the LINCS issues. I got this error now with grompp. I don't think anything else is different other than double precision, but I included the logs for this. ---

[gmx-users] Grompp failed under double precision

We have a workflow going, and I switched to double precision because of the LINCS issues. I got this error now with grompp. I don't think anything else is different other than double precision, but I included the logs for this. --- Program grompp

Re: [gmx-users] Fatal error: 1 particles communicated to PME node 1 are more than a cell length out of the do main decomposition cell of their charge group

Nilesh Dhumal wrote: Hello, I am trying to a run a simulation for dioxin and ionic liquid system (BMI-DCN) in Gromacs 4.0.5 version. The minimization and equilibration (I heat the system at 700, 600, 500 (200 ps, NVT). I run 1 ns for NVT and 4 ns for NPT) went OK. I am trying to run dynami

[gmx-users] Fatal error: 1 particles communicated to PME node 1 are more than a cell length out of the do main decomposition cell of their charge group

Hello, I am trying to a run a simulation for dioxin and ionic liquid system (BMI-DCN) in Gromacs 4.0.5 version. The minimization and equilibration (I heat the system at 700, 600, 500 (200 ps, NVT). I run 1 ns for NVT and 4 ns for NPT) went OK. I am trying to run dynamics for 20 ns but after 3

[gmx-users] Fatal error: 1 particles communicated to PME node 1 are more than a cell length out of the do main decomposition cell of their charge group

Hello, I am trying to a run a simulation for dioxin and ionic liquid system (BMI-DCN) in Gromacs 4.0.5 version. The minimization and equilibration (I heat the system at 700, 600, 500 (200 ps, NVT). I run 1 ns for NVT and 4 ns for NPT) went OK. I am trying to run dynamics for 20 ns but after 3.

Re: [gmx-users] Gromacs-4.0.6 released

Make that gromacs-4.0.7 :-) When yours truly added the automatic apple-64-bit detection from the head branch, I accidentally removed all 3DNow checks too, since that code is no longer supported in the main tree. This caused autoconf to try and build 3DNow kernels by default on all 64bit Linux p

[gmx-users] g_mindist after trjconv -fit give different results

Hi Tsjerk, thanks for the reply. Will the MSD of the molecule also be affected by the fitting. I'm trying to calculate the relative diffusion coefficient of an ion near a protein. For this I thought to first fix the system according to the protein and then calculate the msd of the ion. I noti

[gmx-users] Gromacs-4.0.6 released

Hi, We've just put a maintenance release on the site (find it on www.gromacs.org or directly on ftp.gromacs.org). Basically, this includes a number of minor fixes we've incorporated from Bugzilla the last few months. In particular, the append issues with files >2GB have been fixed, and 32/64 b

Re: [gmx-users] Reducing Standard Error output

>> >> Apparently this code is only used if the app is in verbose mode. So I >> guess we have two choices: >> 1) either find the cause of the lincs warnings > > That is always necessary if you don't want an expensive random number > generator. Your simulation system is ill conditioned, and the lincs

Re: [gmx-users] DNA coarse grain simulation

Hans HEINDL wrote: Are there forcefield parameters available for DNA coarse grain simulations (ideally the forcefields should be compatible with the Martini cg parameters Have you searched the literature? Google turns this up as its third result: dx.doi.org/10.1098/rsif.2008.0239.focus -Ju

[gmx-users] DNA coarse grain simulation

Are there forcefield parameters available for DNA coarse grain simulations (ideally the forcefields should be compatible with the Martini cg parameters Thanks in advance Hans HEINDL -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

Re: [gmx-users] pdb2gmx error

刘文 wrote: hi! I encounter a problen of " Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 426 Fatal error: Residue 'CO' not found in residue topology database" how to solve it? Please search the mailing list archive and the Gromacs wiki when you encounter problems; you wou

[gmx-users] pdb2gmx error

hi! I encounter a problen of " Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 426 Fatal error: Residue 'CO' not found in residue topology database" how to solve it? thank you in advance! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] Questions about hydrogen bond lifetime

Jian Dai wrote: Hi, dear all (especially for David): When reading the paper "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media" and its supplementary material and the code "gmx_hbond.c" for the analysis of hydrogen bond, I got questions: 1. When calculating the autocorrela