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
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
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
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
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
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
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
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
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
*
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
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
-- 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
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?
>>
>>
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:
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-
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
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
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
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.
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
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
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
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
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
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
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.
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