Re: [gmx-users] Secondary structure content

If i remember correctly the DSSP plot should be something like residue # on y-axis, and time on the x-axis, then it is normally a color plot of what secondary structure each residue is in at that time point. Secondary structure content (%) vs time sounds more like a single plot of the fraction

[gmx-users] Fwd: umbrella sampling

-- Forwarded message -- From: Nivedita Rai Date: Fri, Sep 8, 2017 at 9:39 PM Subject: umbrella sampling To: gromacs.org_gmx-users@maillist.sys.kth.se Dear gromacs developers, I am trying to implement umbrella sampling in my work but instead of distance

Re: [gmx-users] residue number in secondary structure plot

On 9/9/17 1:58 PM, Emran Heshmati wrote: Dear Gromacs users I performed a md simulation on apeptide fragment consist of 16 aa . when I analysed its secondary structure content using "gmx do_dssp " command, there was only 15 aa in y-axis in resultig *.eps file format. can anyone explain this

Re: [gmx-users] Protein break after simulation

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.

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Hello Wes, Thanks for your reply. Sorry, I did not understand why we need to turn off charges first and then vdw, if the are performing both steps separately. I was attempting to perform the vdw and charge transformations separately. So for the vdw transformation, if I use c-lambda0=vdw and

[gmx-users] residue number in secondary structure plot

Dear Gromacs users I performed a md simulation on apeptide fragment consist of 16 aa . when I analysed its secondary structure content using "gmx do_dssp " command, there was only 15 aa in y-axis in resultig *.eps file format. can anyone explain this controversy. -- Gromacs Users mailing list *

[gmx-users] Fatal error: domain decomposition

HI, I got a fatal error which running an Ionic liquid simulation under NPT ensemble. What does this error mean and how can I resolve it? Fatal error: There is no domain decomposition for 20 nodes that is compatible with the given box and a minimum cell size of 1.5975 nm Change the number of

Re: [gmx-users] Secondary structure content

Thank you :) Can you please suggest me than what's the last line of scount.xvg file indicates? It is ss(%), what does it mean? Which kind of secondary structure percentage is this? Thank you for your time and help.. On 9 Sep 2017 7:03 p.m., "Justin Lemkul" wrote: > > > On

Re: [gmx-users] Protein break after simulation

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] Fatal error: domain decomposition

On 9/9/17 7:15 AM, Tamisra Pal wrote: HI, I got a fatal error which running an Ionic liquid simulation under NPT ensemble. What does this error mean and how can I resolve it? Fatal error: There is no domain decomposition for 20 nodes that is compatible with the given box and a minimum cell

Re: [gmx-users] Secondary structure content

On 9/9/17 9:30 AM, Smith, Micholas D. wrote: If i remember correctly the DSSP plot should be something like residue # on y-axis, and time on the x-axis, then it is normally a color plot of what secondary structure each residue is in at that time point. Secondary structure content (%) vs

Re: [gmx-users] Protein break after simulation

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] Free Energy Calculations: Error during minimization step.

On Sat, Sep 9, 2017 at 2:09 AM, Abhishek Acharya wrote: > Dear GROMACS users, > > I am trying to estimate the free energy of solvation for a ion. But, I am > facing a problem while running simulations for the deltaG_LJ calculation. > The simulation at vdw_lambda=1.0

Re: [gmx-users] Secondary structure content

I also have same doubt. On 9 Sep 2017 11:13 p.m., "nidhi" wrote: > Thank you :) > Can you please suggest me than what's the last line of scount.xvg file > indicates? > It is ss(%), what does it mean? Which kind of secondary structure > percentage is this? > > Thank you

Re: [gmx-users] Secondary structure content

On 9/9/17 1:43 PM, nidhi wrote: Thank you :) Can you please suggest me than what's the last line of scount.xvg file indicates? It is ss(%), what does it mean? Which kind of secondary structure percentage is this? It should be the fraction of residues of each type of structure. -Justin

Re: [gmx-users] Protein break after simulation

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] Fatal error: domain decomposition

Many thanks Justin On Sat, Sep 9, 2017 at 7:03 PM, Justin Lemkul wrote: > > > On 9/9/17 7:15 AM, Tamisra Pal wrote: > >> HI, >> >> I got a fatal error which running an Ionic liquid simulation under NPT >> ensemble. >> What does this error mean and how can I resolve it? >> >>

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

On Sat, Sep 9, 2017 at 10:10 AM, Abhishek Acharya wrote: > Hello Wes, > > Thanks for your reply. > > Sorry, I did not understand why we need to turn off charges first and then > vdw, if the are performing both steps separately. > > I was attempting to perform the vdw

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

You can do them separately, but the charges need to have been turned off for the molecule you are transforming for the second step when turning off vdw. In other words, all charges must be 0.0 for the molecule in the topology file for the vdw transformation. Is that what you've done? Justin's

[gmx-users] MD of native complex

Hello All, I have done MD of a native pdb structure 2LL7 for 10ns. Looking at the trajectories in PyMOL, I see that in the native structure one of the helix (short separate chain ID) tends to unfold. Is this possible in the simulation of native complexes? Thanks & Regards. -- Gromacs Users

[gmx-users] Listed nonbonded interaction between particles beyond the table limit.

Dear Gromacs experts, I do aware that this question has been repeated many times in the mailing list and I do go through all of answers. However, I still cannot find the answer for my problem. When I run on single node on my laptop, the simulation goes well and the warning does not appear. When I

Re: [gmx-users] Secondary structure content

Thank you all.. On Saturday, September 9, 2017, Justin Lemkul wrote: > > > On 9/9/17 1:43 PM, nidhi wrote: > >> Thank you :) >> Can you please suggest me than what's the last line of scount.xvg file >> indicates? >> It is ss(%), what does it mean? Which kind of secondary

Re: [gmx-users] residue number in secondary structure plot

Than you Justin. I used CHARMM force field. On Sat, Sep 9, 2017 at 10:38 PM, Justin Lemkul wrote: > > > On 9/9/17 1:58 PM, Emran Heshmati wrote: > >> Dear Gromacs users >> I performed a md simulation on apeptide fragment consist of 16 aa . when I >> analysed its secondary

Re: [gmx-users] Protein break after simulation

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:

[gmx-users] Secondary structure content

Dear all, I am confused with 'dssp' output graph i.e "number of residues vs time". Is it also called "secondary structure content(%) vs time" ?? Or it is different term? please, anyone help me to solve this confusion or send me any link contained proper definition of these two. Thanks in

[gmx-users] Free Energy Calculations: Error during minimization step.

Dear GROMACS users, I am trying to estimate the free energy of solvation for a ion. But, I am facing a problem while running simulations for the deltaG_LJ calculation. The simulation at vdw_lambda=1.0 crashes during the steepest-descent minimization step, with the following error.