[gmx-users] Initial cell size is smaller than the cell size limit..

2013-07-21 Thread Kavyashree M
Dear users, While running a ligand bound MD using AMber03 force field. I got the following error after ~ 4.9 ns The initial cell size (1.247705) is smaller than the cell size limit (1.586683), change options -dd, -rdd or -rcon, see the log file for details Initially I ran using 64 nodes (till 3.3

[gmx-users] Persistence length calculation using g_polystat

2013-07-21 Thread Mohan maruthi sena
Dear gmx users, I would like to calculate persistence length of DNA using gromacs command g_polystat . The out put file of persists.xvg contains persistence length in number of bonds and it shows that the average persistence length = 4.3 bonds. How can we convert no of b

[gmx-users] LAMBADA and InflateGRO2

2013-07-21 Thread Atila Petrosian
Dear gromacs users I want to use LAMBADA and InflateGRO2 to create a system containing dopc lipid + cholesterol + drug. When I use ~/lib/lambada/lambada_rc1/lambada -f1 drug.gro -f2 lipid_chol.gro I encountered with Illegal division by zero at /home/karami/lib/lambada/ lambada_rc1/lambada line

Re: [gmx-users] mdrun error

2013-07-21 Thread Justin Lemkul
On 7/21/13 12:18 AM, Collins Nganou wrote: Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --