Dear Dr. Justin, Thank you so much for the reply. Regards ~ Sudha
On Thu, Jan 17, 2019 at 3:41 AM Justin Lemkul <[email protected]> wrote: > > > On 1/15/19 11:29 PM, sudha bhagwati wrote: > > MD_output.tar.gz > > < > https://drive.google.com/file/d/1aJewpvBzeeH4C6o53nCl2qaPTCFDaDeD/view?usp=drive_web > > > > Greetings Sir/Madam > > > > I am running MD simulation using commands listed below- > > > _______________________________________________________________________________________________________________________________________ > > gmx pdb2gmx -ignh -f protein.pdb > > gmx editconf -f ligand.pdb -o ligand.gro > > > > gmx editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0 > > gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro > > > > gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr > > gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL > > -neutral > > > > gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr > > gmx mdrun -v -deffnm em > > > > gmx make_ndx -f em.gro -o index.ndx > > > > gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr > > > > gmx mdrun -v -deffnm nvt > > > > gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o > > npt.tpr > > > > gmx mdrun -v -deffnm npt > > > > gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o > > md_0_20.tpr > > > > gmx mdrun -v -deffnm md_0_20 > > > _____________________________________________________________________________________________________________________________________ > > > > I have attached the tar file for generated output files from complete > > gromacs run. > > The mailing list does not accept attachments. > > > I am not an expert user of gromacs. So which file I can use as state.cpt > > and what is the command to rerun my stopped MD run? > > You asked for files to be called md_0_20 as the prefix, so you will have > md_0_20.cpt as the final checkpoint file. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > [email protected] | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Thanks & regards ~ Sudha Bhagwati -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
