Re: [gmx-users] Protein break after simulation

2017-09-11 Thread ISHRAT JAHAN
no grompp not gives any warning neither i have used -maxwarn option. On Mon, Sep 11, 2017 at 5:26 PM, Justin Lemkul wrote: > > > On 9/11/17 2:43 AM, ISHRAT JAHAN wrote: > >> how can i check whether the structure is whole or not in .tpr file? After >> trjconv whole stage i got

Re: [gmx-users] Protein break after simulation

2017-09-11 Thread Justin Lemkul
On 9/11/17 2:43 AM, ISHRAT JAHAN wrote: how can i check whether the structure is whole or not in .tpr file? After trjconv whole stage i got broken structure. This is beyond just a "broken" structure.  No amount of PBC manipulation will fix this; it's as if the topology wasn't sound and you

Re: [gmx-users] Protein break after simulation

2017-09-11 Thread ISHRAT JAHAN
Here i am providing you the link of protein structure https://we.tl/X4yEyZq2aR On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul wrote: > > > On 9/10/17 3:27 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> I have used all the commands given in the link provided by you but unable >> to

Re: [gmx-users] Protein break after simulation

2017-09-11 Thread ISHRAT JAHAN
how can i check whether the structure is whole or not in .tpr file? After trjconv whole stage i got broken structure. On Sun, Sep 10, 2017 at 9:00 PM, Mark Abraham wrote: > Hi, > > You seem to reporting that your system isn't whole. Is it whole after the > trjconv

Re: [gmx-users] Protein break after simulation

2017-09-10 Thread Mark Abraham
Hi, You seem to reporting that your system isn't whole. Is it whole after the trjconv -whole stage? Is the structure in that .tpr whole? Mark On Sun, Sep 10, 2017 at 9:27 AM ISHRAT JAHAN wrote: > Dear Justin > I have used all the commands given in the link provided by you

Re: [gmx-users] Protein break after simulation

2017-09-10 Thread Justin Lemkul
On 9/10/17 3:27 AM, ISHRAT JAHAN wrote: Dear Justin I have used all the commands given in the link provided by you but unable to get the solution. commands used by me are- trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole -n prtn_drg.ndx trjconv -f prtn_md_whole.xtc -s

Re: [gmx-users] Protein break after simulation

2017-09-10 Thread ISHRAT JAHAN
Dear Justin I have used all the commands given in the link provided by you but unable to get the solution. commands used by me are- trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole -n prtn_drg.ndx trjconv -f prtn_md_whole.xtc -s prtn_md.tpr -o prtn_md_cluster.xtc -pbc

Re: [gmx-users] Protein break after simulation

2017-09-09 Thread Justin Lemkul
On 9/9/17 10:12 AM, ISHRAT JAHAN wrote: Actually my final .gro file is totally broken into smaller parts when i load it in vmd, for this what will i do? Again, everything you need is in the link I provided. -Justin On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul wrote:

Re: [gmx-users] Protein break after simulation

2017-09-09 Thread ISHRAT JAHAN
Actually my final .gro file is totally broken into smaller parts when i load it in vmd, for this what will i do? On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul wrote: > > > On 9/9/17 10:05 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> commands which i have used are given belown-

Re: [gmx-users] Protein break after simulation

2017-09-09 Thread Justin Lemkul
On 9/9/17 10:05 AM, ISHRAT JAHAN wrote: Dear Justin commands which i have used are given belown- gmx trjconv -f protein_out.xtc -s protein_md.tpr -o protein_nojump.xtc -pbc nojump gmx trjconv -f protein_nojump.xtc -s protein_md.tpr -o protein_cluster.xtc -pbc cluster gmx trjconv -f

Re: [gmx-users] Protein break after simulation

2017-09-09 Thread ISHRAT JAHAN
Dear Justin commands which i have used are given belown- gmx trjconv -f protein_out.xtc -s protein_md.tpr -o protein_nojump.xtc -pbc nojump gmx trjconv -f protein_nojump.xtc -s protein_md.tpr -o protein_cluster.xtc -pbc cluster gmx trjconv -f protein_cluster.xtc -s protein_md.tpr -o

Re: [gmx-users] Protein break after simulation

2017-09-09 Thread Justin Lemkul
On 9/9/17 1:50 AM, ISHRAT JAHAN wrote: Dear all, I have done 100ns md simulation of protein with drug using amber99sb.ff with gromacs-5.1.4 version. After simulation i found my protein broken into smaller parts in .gro file but when i load the final xtc file to pr.gro molecule does not break.

[gmx-users] Protein break after simulation

2017-09-08 Thread ISHRAT JAHAN
Dear all, I have done 100ns md simulation of protein with drug using amber99sb.ff with gromacs-5.1.4 version. After simulation i found my protein broken into smaller parts in .gro file but when i load the final xtc file to pr.gro molecule does not break. I have applied -pbc nojump ,cluster and