Re: [gmx-users] LINCS Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. How did you energy minimze your structure? What was the output of mdrun during energy minization, especially the last line with Fmax, Epot etc.? I should look like this: Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, atom= 78754 Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, atom= 13032 Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, atom= 13032 Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS Warning using mdrun
Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
