On 1/17/20 11:01 PM, Ashma Khan wrote:
Thank for your suggestion Alessandra
I have applied the pbc conditions on my system in steps as follows:
1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
ful
Thank for your suggestion Alessandra
I have applied the pbc conditions on my system in steps as follows:
1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
full_md_nojump.xtc
3. gmx trjconv -f full_md_no
Hi,
On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan wrote:
> Thank you for your suggestion Alessandra Villa
> I have applied all types of pbc conditions but my one peptide is diffusing
> away from another peptide in case of dimer after half of the simulation
> time and rmsd is coming out 100 Angstrom
Thank you for your suggestion Alessandra Villa
I have applied all types of pbc conditions but my one peptide is diffusing
away from another peptide in case of dimer after half of the simulation
time and rmsd is coming out 100 Angstrom after that time which is very
high. Please suggest me what shoul
Hi,
I suggest to visualize your trajectory. Maybe one of the peptide is
diffusing away from the other.
Or the one peptide is jumping in and out or moving out the box.
If it is the case, here you found some trjconv workflow
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condition
Dear all,
I have calculated the c-alpha RMSD of dimer having 7 residues peptide each
by using command gmx rms. But the calculated RMSD 14 Angstorm is very high,
although I have applied all pbc conditions. Anybody can suggest me why so
much high RMSD is coming or is it possible.
--
Ashma Khan
Rese
