macs-user.biotalk.us/salt-bridge-calculations-t91121.html
Then there is the "g_saltbr" tool. I am confused now as to what to use. If
I want to use "g_dist" how should I proceed ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Hi Antara
Did you check the plot of the potential energy against the simulation time
? You can visualize the convergence of your energy minimisation from the
above plot.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
On 2/9/15 7:41 AM, Antara mazumdar wrote:
> i
:
HISTO
<https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web>
Kindly help.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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"restraint
forces" for DNA/protein systems ?
Regarding window setup, is it the spacing of the windows ?
Except for simulation time is there any other method for increasing
sampling ?
I have read the manual but could not find anything. I am searching in the
web also.
Thanks & Regards
Agn
the 12600 units of force constant as it is
very high and there is no validation. I found some literature using 1000 -
10,000 kJ/mol/nm^2 force constants for proteins.
Any suggestions please ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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drive_web>
I think the shape of the histograms is OK now, they dont appear rocky and
broken. I suppose I need proper overlap at present with regards to window
spacing and all.
Kindly review and suggest.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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e and
error ??
On 2/19/15 9:50 PM, Agnivo Gosai wrote:
> Dear Users
>
> This is my earlier post wherein I received useful suggestion from Dr.
> Lemkul.
>
> http://comments.gmane.org/gmane.science.biology.gromacs.user/74659
>
> Earlier for my system , I was doing a
e PMF converged from
the standpoint of error analysis.
What are your opinions ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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erv_pmci.c:388):
error waiting for event
[mpiexec@node094] main (./ui/mpich/mpiexec.c:718): process manager error
waiting for completion
Can anyone please help with this I am waiting for a reply in this forum
after which I will take it up with the cluster admins.
Thanks & Regards
Agnivo Gosa
I think it is well explained and should work with GROMACS 4.6.7. Any
suggestions ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Ca
ore nodes. However there is no output when np = 24 or 32 and such like.
I dont get what is going on. I have contacted my university HPC group and
described the problem. Lets see what happens.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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*
trator.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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/ns)
Performance: 21.3931.122
So , I have bad performance.
Now I am using only MPI for running the jobs.
Any suggestions on performance improvement ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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ing simulation ?
Or there is some other method ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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advisable ?
Kindly suggest.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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results seem to match published
literature. So I am happy.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
On Wed, Mar 4, 2015 at 2:38 PM, Agnivo Gosai
wrote:
> Dear Users
>
> I am using umbrella sampling to calculate free energy of binding between
> two biomolecu
motion removal for the whole system.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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thermostat , GROMACS will give error
message. So how do I fix this problem ?
Or, should I freeze the protein instead and use a thermostat on the solvent
?
I am trying both of these as I write this mail.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Best,
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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error:
2936 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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comm-mode = Linear
comm-grps = System
Plz have a look.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can
Dr. Lemkul
Thanks for such an easy fix to my problem. I guess I have been doing all
sort of weird stuff since last night instead of thinking logically and
reading the relevant portion of the manual.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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or e.g.) and then do a NVT
equilibration at 300 K?
Kindly suggest.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can't
input.pdb -o complex.gro -p topol.top
and I use AMBER99SB ( with parmbsc0 for the DNA part ) , TIP3P water.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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input.pdb -o complex.gro -p topol.top
and I use AMBER99SB ( with parmbsc0 for the DNA part ) , TIP3P water.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Justin & Tsjerk
So, do you think the equilibration error is because of this long bond ? I
was thinking as the error message was about water molecules/atoms , the
source was something else.
I will get back after I fix this warning in a proper and acceptable way.
Thanks & Regards
Agni
docs.google.com/file/d/0B-U8uULVZjfRQ0JzdVZlcG1YWjQ/edit?usp=drive_web>
For the 1st image VMD did not show the secondary structures of the protein
as a STRIDE warning and error came. However the energy minimized structure
did not show such warnings.
Any suggestions
Thanks & Reg
229 and 230.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Dr. Lemkul,
Thank you very much for taking time to review my problem. I am sure this
forum post will help all the new members in resolving related issues.
I will post again after attempting another equilibration.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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other software like Adobe / Inkscape to edit the image?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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rstand the fractional charge for the protein.
Any suggestions ???
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can
interpolation
fourierspacing = 0.12 ; grid spacing for FFT
I would still like to use 64 processes for the mdrun. Any suggestions
please.
I am thinking of playing with -rcon. But I am not sure if it will affect
the accuracy of the simulation.
Thanks & Regards
Agnivo Gosai
Grad Student,
to equilibrate more ? I used AMBER99SB/TIP3P.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
On Mon, Nov 16, 2015 at 1:49 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
> groma
.xtc file so that the pull force
and the COM separation are of same vector lengths? or do I need to add
something to my .mdp file to be able to do it ? Like , nstfout ??
I did not download the trr file from the cluster as it is very huge !
Kindly help please.
Thanks & Regards
Agnivo Gosai
-extension
distance in the mdp file if you are really sure that is the reason.
I am seeing this for the 1st time , kindly help in understanding.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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tps://drive.google.com/file/d/0B-U8uULVZjfRaUhmNXB0RU9rZk0/view?usp=drive_web>
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can't
; Include [atomtypes]
#include "myligand_atomtypes.itp"
...
So should I look at the parameters for AMBER99SB ?Kindly suggest.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State U
n or shell script ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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r comments then do I need to show
equivalent simulation data as in the original ff paper.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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cut-off of 0.8 nm for all non-bonded interactions.
Please explain.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can't post?
, I was
thinking if I could skip that step for now.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can't post?
ocedure to conduct the
simulations.But now I am confused. Kindly comment.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can
simulation and the result is
almost identical. I think as my pulling code is same I am getting more or
less same result.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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, please
check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>*
-
I am not sure as to how to carry on to the next level. Any insight is
very much appreciated.
Best Regards,
Agnivo
Dear Dr. Justin
Thank you for the insight . My problem is solved.
Best
Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State University
On Sat, Aug 9, 2014 at 5:00 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mai
64-Bit
Could anyone please tell me what version of GROMACS I should try installing
??
Thanks & Regards
Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State University
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the topology file generated by
"pdb2gmx" contains the total electron charge value for a molecule.
I was wondering if this can be used to get the charge value for Thrombin at
physiological pH.
Thanks & Regards
Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State Universi
Dear Users
I am facing a problem while compiling the GROMACS source code in my
university cluster. I am laying down my installation procedure step by step
:-
1. Downloaded fftw 3.3.4
2. exported paths of C-compiler and Fortran-compiler
3. Used the following command line to configure FFTW
*./confi
721 (2005))
>
> You should look if the pH, which you need, is > o < that the corresponding
> value of pka and then you should determine the protonation state of the
> protein . The pdb2gmx program has the option of being interactive with
> respect to those aminoacids that h
Dr. Lemkul
Thanks for your valuable suggestion. I used make distclean and could
successfully install the serial version of GROMACS 4.5.6 in my university
cluster
After that I used "make distclean" again and proceeded with compiling the
parallel version of mdrun in a separate directory
However wh
Dear Gromacs Users
I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO )
. I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported
into it. I had cleaned the PDB file off crystal waters and a small chemical
ligand ( which I dont require ) before passing it t
er of residues have increased and the total no. of atoms
have also increased.* *I have also observed the same thing while completing
Dr. Lemkul's tutorials. Why does this happen ? I have searched the web but
could not find any satisfactory answer.*
Thanks & Reagrds
Agnivo Gosai
Graduate Student
Iowa
also consulted the error section
of the GROMACS documentation but could not understand.
Thanks & Regards,
Agnivo Gosai
Grad. Student , Iowa State University
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meaning of the term "Err. Est" and
"Tot-drift". I have consulted the GROMACS manual but I am not satisfied and
failed to understand the physical significance.
Kindly explain.
Thanks & Regards
Agnivo Gosai
Grad. Student, ISU
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* Please sea
lated."
Are there any guidelines for assigning the COM position of my biomolecule
complex and the x,y,z dimensions of my simulation box keeping in mind the
above explanation.
Or I should go about it in a trial and error basis?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State Universit
t the end?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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*
cture / coordinate ) file and named
the DNA chain as Chain_D and the two protein chains as Chain_P.
I believe that this is the correct approach before I run the pulling
simulation.
I request the experienced users to suggest and comment on my understanding.
Thanks & Regards
Agnivo Gosai
Gra
file having the vectors listed in the last
line.
My question is :- Is the last line has to do anything with the "size" of
the molecule ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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4.5.7 single precision.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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set pressure.
*So should I carry out the simulation for a longer time ?? Or should I use
a different barostat on the next NPT run or do it in a fresh NPT run.*
*Kindly suggest.*
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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suggestions please ??
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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to achieve the reference set pressure.
*So should I carry out the simulation for a longer time ?? Or should I use
a different barostat on the next NPT run or do it in a fresh NPT run.*
*Kindly suggest.*
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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PMF based
on binding energy.
Kindly shed some light on this issue , please. Pardon for my ignorance.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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kMXNoYW8/edit?usp=drive_web>
Could anybody suggest why the reference pressure is not being reached ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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hainlength reset to 1
My question is how will this affect my simulations ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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protein complex as discussed in
similar posts in the gmx forums.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
On Mon, Nov 3, 2014 at 6:37 PM, Agnivo Gosai
wrote:
> Dear Users
>
> I am following the Umbrella Sampling tutorial by Dr. Lemkul. I am using
> GROMA
& Regards
Agnivo Gosai
Grad Student, Iowa State University.
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during the production run ?
Kindly explain.
My reasoning so far is inferential , but I am searching literature on this
matter.
On 11/4/14 5:37 PM, Agnivo Gosai wrote:
> Dear Users
>
> I have followed several GROMACS tutorials , specially the excellent Lemkul
> tutorials. I have seen
provide suggestions.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
On 11/7/14 4:20 PM, Agnivo Gosai wrote:
> Dear Users
>
> I checked and found that the CMAKE version installed in my university
> cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher.
> So I installed
.kth.se>
Cc:
Date: Sat, 08 Nov 2014 09:19:14 +0800
Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
What he meant was to specify full path of your cmake, i.e.
/work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY. (and so
on); instead of just typing cmake .. -DGMX_FFT
http://lmgtfy.com/?q=difference+between+gcc+and+g%2B%2B
http://lmgtfy.com/?q=gcc+compiler+installation+linux
<
https://mail.google.com/mail/u/0/?ui=2&ik=4d6c0a5051&view=att&th=149643f024d7d537&attid=0.1&disp=safe&realattid=f_i1wzdfrg0&zw
>
On Sun, Nov 9, 2014
;&1 | tee make-install.out
> and share the resulting make-install.out file (use pastebin or similar).
>
> Cheers,
> --
> Szilárd
>
>
> On Sun, Nov 9, 2014 at 8:21 PM, Agnivo Gosai
wrote:
>> Dear Users
>>
>> I have tried installing both versions 4.6.5 and
it crashes it is
installing in a directory which contains '/gromacs' about 300 times.
My first guess is that you are installing in the same directory where
your build (and source tree?) is. Is that the case?
--
Szilárd
On Mon, Nov 10, 2014 at 12:31 AM, Agnivo Gosai
wrote:
> Dear Users
&
53454 atoms that were outside the box
OMP: Error #178: Function pthread_getattr_np failed:
OMP: System error #12: Cannot allocate memory
Aborted
Now upon searching on the web it seems to be an OpenMP error. Again I am in
a fix which I have little or no idea about.
Thanks & Regards
Agnivo Gosai
09 +0100
Subject: Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster
On Mon, Nov 10, 2014 at 2:17 AM, Justin Lemkul wrote:
>
>
> On 11/9/14 8:15 PM, Agnivo Gosai wrote:
>
>> Dear Users
>>
>> Firstly thanks (specially Drs. Szilard and Mark ) for helping me o
in the GROMACS manual , however I
would hugely benefit from the suggestions by the forum members.
Thanks & Regard
Agnivo Gosai
Grad Student, Iowa State University.
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interactions on a script. Can I type
group1 , group4 , | , q on a .txt file and pass it onto make_ndx in the
script. I have not seen myself , but I am speculating. Please bear with my
ignorance.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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i from version 4.6.1 has not been properly compiled
to run on several nodes in the cluster. However I would like to do it to
speed up my simulations.
Any suggestions , please ??
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
-- Forwarded message --
From: Mark
hould I simultaneously increase my simulation time for umbrella
sampling to say 5 ns from 1 ns ?
Kindly suggest
----
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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*
; Regards
Agnivo Gosai
Grad Student, Iowa State University.
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tal
pulling distance) > 0.49 times 15 nm ( length of box in z direction ) and
is contributing to the error. But this has been the same in cases 1 and 2
also. Hence I am getting confused.
Any suggestions , please ??
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Forwarded message ------
From: Agnivo Gosai
Date: Tue, Nov 25, 2014 at 1:44 PM
Subject: SMD - Pulling Error in mdrun 0.49 times box size
To: gromacs.org_gmx-users@maillist.sys.kth.se
Dear Users
I have put my molecule complex in a box having dimensions 7.5 7.5 15 . The
center of the molecul
;energygrps" in a .mdp file.
I checked the mdout.mdp generated during grompp+mdrun and found that
energygrps = (blank). In that case what is happening ? I use version 4.6.7
and also checked the manual but could not satisfy myself.
Kindly answer.
Thanks & Regards
Agnivo Gosai
Grad Studen
/0B-U8uULVZjfRMVRINHNQOURCOWc/edit?usp=drive_web>
PMF2.png
<https://docs.google.com/file/d/0B-U8uULVZjfRWXdXVGVlNXU3Rm8/edit?usp=drive_web>
pmfintegrated.png
<https://docs.google.com/file/d/0B-U8uULVZjfROVBaaGlxWThZdEk/edit?usp=drive_web>
Kindly explain the possible reason behind this.
Thank
meone say
what is going on. Lookwise the pmfintegrated.xvg is so smooth that I
am tempted to use it , but I don not know why and how it is generated.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
On Mon, Dec 8, 2014 at 11:35 AM, Agnivo Gosai
wrote:
> Dear Users
>
my
system. I neutralized the system with Na and Cl ions such that the final
conc is 0.1 M.
b) In general is my procedure a correct way of using "g_hbond" ?
Kindly help.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Please sea
(8) ./dssp-2.0.4-linux-i386 -i pull1.pdb -o pull1.dssp
This works fine. But I want to use GROMACS to generate plots and figures
with its do_dssp command.
Kindly help me to find a solution.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Pl
Hello
I am sorry for wasting your time. The online GROMACS help is enough to fix
my problem.
I am giving it below.
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
The problem is fixed now!!
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
On Thu, Jan 29,
cropped up in my mind.
Do I need to provide an index file containing only the hydrophobic residues
of the protein and the ligand ?
Or, just a normal index file with all the protein residues and ligand
residues in two separate groups will do the job?
Thanks & Regards
Agnivo Gosai
Grad Student,
ucture but still I am
not able to figure out an answer to his question.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can
there any
literature available. I am sorry if I am asking for too much.
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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* Can't p
was thinking of extracting every frame (using trjconv) from my total of
501 frames and running g_hbond on each of the frames. But that seems to be
a laborious process. Is there any way out ?
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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