Re: [gmx-users] regarding changing the scale from ps to ns

[Dallas Warren]

What didn't work? Highly recommend with things like this that you copy and
paste the exact command you tried and what the output was. Vague references
to it not working is not helpful to those looking to give advice on what to
do.

The suggested command by Reza was something like:

gmx trjconv -f input_pstime.xtc -o output_nstime.xtc -tu ns

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 29 Aug 2019 at 19:34, sudha bhagwati 
wrote:

> Thanks for the reply.
> But it did not work for me. Can you please write the command line, it would
> be much helpful.
> Thank you.
>
> On Thu, Aug 29, 2019 at 2:33 PM Mohammadreza Niknam Hamidabad <
> jj700phys...@gmail.com> wrote:
>
> > Hi,
> > I'm currently using Gromacs 2018 and I'm not quite sure about the 5.x
> > version. The gyrate module doesn't have -tu flag so my suggestion is that
> > you convert your .xtc file to a new xtc file with trjconv -tu ns then use
> > gyrate for your calculation.
> > I hope you find it useful.
> >
> > Best regards,
> > Reza
> >
> >
> > On Thu, Aug 29, 2019 at 7:38 AM sudha bhagwati 
> > wrote:
> >
> >> Hi,
> >>
> >> I am using the GROAMCS 5.1.4 version.
> >>
> >>
> 
> >> Running the commands below:
> >>
> >>
> >> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
> >> *OR*
> >> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
> >>
> >>
> >> Error while executing commands:
> >>
> >> *Error in user input:*
> >>
> >> *Invalid command-line optionsUnknown command-line option -tu*
> >>
> >>
> 
> >>
> >> I want to generate my plots for nanosecond scale. Could you please help
> me
> >> out with this issue. I'd be really grateful to you.
> >>
> >> Thank you.
> >>
> >>
> >> --
> >> Thanks & regards
> >> ~
> >> Sudha Bhagwati
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
>
> --
> Thanks & regards
> ~
> Sudha Bhagwati
> --
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Re: [gmx-users] Why protein structure is outside of lipid environment after MD simulation using Gromacs?

[Dallas Warren]

http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 29 Aug 2019 at 14:35, Muthusankar  wrote:

> Can anyone guide me,
> First time, I run the program of MD simulation of Membrane environment
> using gromacs software.
> My protein is an integral membrane protein. First, I have prepared the
> protein.PDB using OPM server and CHARMM-GUI (SDPC lipid bi-layer) membrane
> builder. Then I have run MD simulation by gromacs software. I have
> visualized equilibration output file and the protein structure was properly
> fit with lipid environment. Then I run the program of MD production at
> 10ns, I got the output file of .gro. I have converted .gro into .pdb file
> and visualize the pymol software. The protein structure is outside of the
> lipid environment (far away). I don't know how to fix the problem.
>
> --
> With regards
> *Dr. Muthu Sankar Aathi*
> *ICMR Post-Doctoral Fellow (ICMR-PDF),*
> Biomedical Informatics Centre,
> ICMR-National Institute for Research in Reproductive Health (NIRRH),
> Parel, Mumbai-400 012, India.
>
> Email: muthubioinf@gmail.c om
> Mobile No.  +91 9080444540
> --
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[gmx-users] simulation termination problem

[Prabir Khatua]

Hello Gromacs users,

I am trying to simulate a system of atom size 3,58,973 in gromacs 5.1.5.
However, my simulation is being terminated in between with the following
error.

File input/output error:
Cannot rename checkpoint file; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I did not find any solution with respect to the error I was having in the
mentioned website. What I found was related to memory issue. I do not know
whether this is the same issue.
Please note that I was successfully able to run another simulation of a
system having relatively less number of atoms with same script. The run
command that I used for the simulation was

mpirun -np 48 gmx_mpi mdrun -ntomp 1 -deffnm npt

I ran both the simulations on two nodes having 24 cpu cores in each one of
the nodes.
I am also not able to figure out one issue. The log file of the system
where the simulation was successfully completed showed

Running on 2 nodes with total 48 cores, 48 logical cores, 0 compatible GPUs
  Cores per node:   24
  Logical cores per node:   24
  Compatible GPUs per node:  0

However, in the unsuccessful case, the log file showed

Running on 1 node with total 24 cores, 24 logical cores

Thus, it looks like the simulation was running on single node although I
asked it to run on two nodes. I have no idea how to fix this issue. Please
help me fix this issue or what I am doing wrong.

Thanks in advance,

Prabir

-- 

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
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[gmx-users] Fatal error: A coordinate in file box.gro does not contain a '.'

[Edjan Silva]

This error occurred while typing the following command:

gmx solvate -cp box.gro -cs spc216.gro -o box_sol.gro -p topol.top

basically what happened was that all the coordinates that were in my
box.gro file were replaced by the word "-nan".

I've never seen anything like this. can anyone tell why this error occurs?
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[gmx-users] [ERROR] NI+2 in gromacs simulations

[Edjan Silva]

I inserted the following parameters in the aminoacids.rtp file:


[ NI ]
 [ atoms ]
NI   opls_411   2.000 0



However, instead of the pdb2gmx command keeping the 2 atoms of NI + 2, two
atoms of Nitrogen are added.

Did I enter the parameters wrong?
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Re: [gmx-users] MDrun Slow!

[Mark Abraham]

Hi,

Please do check out the install guide for advice on how to build for the
hardware you plan to run on. The defaults will just do the right thing for
you :-)

Mark

On Thu, 29 Aug 2019 at 14:26, Quin K  wrote:

> Hi
> When I do a mdrun it gives me a message saying,
>
> Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see
> log).
> The current CPU can measure timings more accurately than the code in
> gmx mdrun was configured to use. This might affect your simulation
> speed as accurate timings are needed for load-balancing.
> Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake
> option.
> Reading file nvt.tpr, VERSION 2018.1 (single precision)
> Changing nstlist from 10 to 80, rlist from 1.2 to 1.328
>
> I noticed that mdrun is running very slow how can I use this option and
> make the process faster?
>
> *How do I turn GMX_USE_RDTSCP=ON ??*
> Thanks in advance
> Regards!
> --
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Re: [gmx-users] regarding changing the scale from ps to ns

[sudha bhagwati]

Thanks for the reply.
But it did not work for me. Can you please write the command line, it would
be much helpful.
Thank you.


On Thu, Aug 29, 2019 at 2:33 PM Mohammadreza Niknam Hamidabad <
jj700phys...@gmail.com> wrote:

> Hi,
> I'm currently using Gromacs 2018 and I'm not quite sure about the 5.x
> version. The gyrate module doesn't have -tu flag so my suggestion is that
> you convert your .xtc file to a new xtc file with trjconv -tu ns then use
> gyrate for your calculation.
> I hope you find it useful.
>
> Best regards,
> Reza
>
>
> On Thu, Aug 29, 2019 at 7:38 AM sudha bhagwati 
> wrote:
>
>> Hi,
>>
>> I am using the GROAMCS 5.1.4 version.
>>
>> 
>> Running the commands below:
>>
>>
>> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
>> *OR*
>> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
>>
>>
>> Error while executing commands:
>>
>> *Error in user input:*
>>
>> *Invalid command-line optionsUnknown command-line option -tu*
>>
>> 
>>
>> I want to generate my plots for nanosecond scale. Could you please help me
>> out with this issue. I'd be really grateful to you.
>>
>> Thank you.
>>
>>
>> --
>> Thanks & regards
>> ~
>> Sudha Bhagwati
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>

-- 
Thanks & regards
~
Sudha Bhagwati
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[gmx-users] MDrun Slow!

[Quin K]

Hi
When I do a mdrun it gives me a message saying,

Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see
log).
The current CPU can measure timings more accurately than the code in
gmx mdrun was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake
option.
Reading file nvt.tpr, VERSION 2018.1 (single precision)
Changing nstlist from 10 to 80, rlist from 1.2 to 1.328

I noticed that mdrun is running very slow how can I use this option and
make the process faster?

*How do I turn GMX_USE_RDTSCP=ON ??*
Thanks in advance
Regards!
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Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Navneet Kumar Singh]

Yeah -nb cpu
Running on cpu.

On Thu, 29 Aug 2019, 17:33 Mark Abraham,  wrote:

> Hi,
>
> Did you try doing em with the flag I mentioned? Simulation won't need any
> change.
>
> Mark
>
> On Mon., 26 Aug. 2019, 22:25 Navneet Kumar Singh, 
> wrote:
>
> > Thank You Sir.
> >
> > Again installed gromacs2016.6 (final version from gromacs2016.x).
> > Throwing same error(HtoD cudaMemcpyAsync failed: invalid argument)
> >
> > . Its running on CPU, but not on GPU. Work of 3 days will take 15 days.
> > Already completed simulation for other complexes. This complex creating
> > problem due to vsites3. PLEASE HELP DEADLINE IS APPROACHING.
> >
> > On Tue, Aug 27, 2019 at 12:23 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > If you have a reason to have to use 2016.x, then please get the latest
> > > version (which is always advisable when starting new work) because this
> > > issue is fixed there. You also don't have to run energy minimization on
> > > GPUs, so you could just append -nb cpu to your mdrun command line to
> > avoid
> > > the problem.
> > >
> > > Mark
> > >
> > > On Mon, 26 Aug 2019 at 20:44, Navneet Kumar Singh <
> navneet...@gmail.com>
> > > wrote:
> > >
> > > > Currently I am using only gromacs16.5. As this have *"PLEASE NOTE*
> that
> > > the
> > > > current versions do support lone pair construction on halogens,
> however
> > > the
> > > > current construction is only compatible with GROMACS-2016.x and by
> > using
> > > > gmx grompp -maxwarn 1 to override the warning about lone pair
> > > > construction."
> > > >
> > > > I was unable to understand this "For all other GROMACS versions, you
> > will
> > > > have to manually edit the topology to use "3fad" construction and
> > > > appropriate atom numbers."as I was using 2018.4. So I switched to
> > > > version-16. But now trapped in this HtoD cudaMemcpyAsync failed:
> > invalid
> > > > argumenterror.
> > > >
> > > > On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You're running 2016.x which had a bug, not the 2018.x you thought
> you
> > > > were
> > > > > using. Use GMXRC or your cluster's modules to select the version
> you
> > > want
> > > > > to use in the terminal or script that you want to use.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh <
> > > navneet...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > What kind of error is this. Previously Gromacs 2018.4 version was
> > > > running
> > > > > > fine using GPU. But Now this error I am getting.
> > > > > >
> > > > > > _
> > > > > >
> > > > > > gmx mdrun -v -deffnm em
> > > > > >   :-) GROMACS - gmx mdrun, 2016.5 (-:
> > > > > >
> > > > > > GROMACS is written by:
> > > > > >  Emile Apol  Rossen Apostolov  Herman J.C. Berendsen
> Par
> > > > > > Bjelkmar
> > > > > >  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
> > > > > Groenhof
> > > > > >  Christoph Junghans   Anca HamuraruVincent Hindriksen
> Dimitrios
> > > > > > Karkoulis
> > > > > > Peter KassonJiri Kraus  Carsten Kutzner  Per
> > > > Larsson
> > > > > >   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
> > > > Marklund
> > > > > >Teemu Murtola   Szilard Pall   Sander Pronk
> Roland
> > > > Schulz
> > > > > >   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> > > > > Tieleman
> > > > > >   Teemu Virolainen  Christian WennbergMaarten Wolf
> > > > > >and the project leaders:
> > > > > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der
> > > Spoel
> > > > > >
> > > > > > Copyright (c) 1991-2000, University of Groningen, The
> Netherlands.
> > > > > > Copyright (c) 2001-2017, The GROMACS development team at
> > > > > > Uppsala University, Stockholm University and
> > > > > > the Royal Institute of Technology, Sweden.
> > > > > > check out http://www.gromacs.org for more information.
> > > > > >
> > > > > > GROMACS is free software; you can redistribute it and/or modify
> it
> > > > > > under the terms of the GNU Lesser General Public License
> > > > > > as published by the Free Software Foundation; either version 2.1
> > > > > > of the License, or (at your option) any later version.
> > > > > >
> > > > > > GROMACS:  gmx mdrun, version 2016.5
> > > > > > Executable:   /usr/local/gromacs/bin/gmx
> > > > > > Data prefix:  /usr/local/gromacs
> > > > > > Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
> > > > > > Command line:
> > > > > >   gmx mdrun -v -deffnm em
> > > > > >
> > > > > >
> > > > > > Back Off! I just backed up em.log to ./#em.log.7#
> > > > > >
> > > > > > Running on 1 node with total 16 cores, 32 logical cores, 1
> > compatible
> > > > GPU
> > > > > > Hardware detected:
> > > > > >   CPU info:
> > > > > > Vendor: Intel
> > > > > >   

Re: [gmx-users] energy minimization

[Mark Abraham]

Hi,

Typical force fields will have negative energies at minimize
configurations, but my guess is that your initial configuration has some
serious problem. Did you visualise the minimization start and end points?

Mark

On Tue., 27 Aug. 2019, 18:52 Dhrubajyoti Maji,  wrote:

> Dear gromacs users,
>  I am doing energy minimization of a neat urea system. When I set emtol =
> 10 the following result is obtained  :
> Steepest Descents converged to machine precision in 33995 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  6.7910172e+04
> Maximum force =  7.8070724e+01 on atom 353
> Norm of force =  3.1714432e+00
> and average energy is
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Potential   72421.6   250014229.1   -16147.4
>  (kJ/mol)
> And when I set emtol=100 the following result is obtained :
> Steepest Descents converged to Fmax < 100 in 12573 steps
> Potential Energy  =  7.1502609e+04
> Maximum force =  8.5925835e+01 on atom 2713
> Norm of force =  5.0333209e+00
> and average energy is
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Potential   77654.4   360022408.3   -22901.6
>  (kJ/mol)
> In both cases the energy is well converged but not less than zero. Does
> only convergence of potential energy (not negative) guarantee the
> completion of EM process ? If so then what emtol value should  I use ?
> Any help will be highly appreciated. Thanks for your time.
> Best regards
> Dhrubajyoti Maji
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Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

[Mark Abraham]

Hi,

Did you try doing em with the flag I mentioned? Simulation won't need any
change.

Mark

On Mon., 26 Aug. 2019, 22:25 Navneet Kumar Singh, 
wrote:

> Thank You Sir.
>
> Again installed gromacs2016.6 (final version from gromacs2016.x).
> Throwing same error(HtoD cudaMemcpyAsync failed: invalid argument)
>
> . Its running on CPU, but not on GPU. Work of 3 days will take 15 days.
> Already completed simulation for other complexes. This complex creating
> problem due to vsites3. PLEASE HELP DEADLINE IS APPROACHING.
>
> On Tue, Aug 27, 2019 at 12:23 AM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > If you have a reason to have to use 2016.x, then please get the latest
> > version (which is always advisable when starting new work) because this
> > issue is fixed there. You also don't have to run energy minimization on
> > GPUs, so you could just append -nb cpu to your mdrun command line to
> avoid
> > the problem.
> >
> > Mark
> >
> > On Mon, 26 Aug 2019 at 20:44, Navneet Kumar Singh 
> > wrote:
> >
> > > Currently I am using only gromacs16.5. As this have *"PLEASE NOTE* that
> > the
> > > current versions do support lone pair construction on halogens, however
> > the
> > > current construction is only compatible with GROMACS-2016.x and by
> using
> > > gmx grompp -maxwarn 1 to override the warning about lone pair
> > > construction."
> > >
> > > I was unable to understand this "For all other GROMACS versions, you
> will
> > > have to manually edit the topology to use "3fad" construction and
> > > appropriate atom numbers."as I was using 2018.4. So I switched to
> > > version-16. But now trapped in this HtoD cudaMemcpyAsync failed:
> invalid
> > > argumenterror.
> > >
> > > On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > You're running 2016.x which had a bug, not the 2018.x you thought you
> > > were
> > > > using. Use GMXRC or your cluster's modules to select the version you
> > want
> > > > to use in the terminal or script that you want to use.
> > > >
> > > > Mark
> > > >
> > > > On Mon, 26 Aug 2019 at 20:34, Navneet Kumar Singh <
> > navneet...@gmail.com>
> > > > wrote:
> > > >
> > > > > What kind of error is this. Previously Gromacs 2018.4 version was
> > > running
> > > > > fine using GPU. But Now this error I am getting.
> > > > >
> > > > > _
> > > > >
> > > > > gmx mdrun -v -deffnm em
> > > > >   :-) GROMACS - gmx mdrun, 2016.5 (-:
> > > > >
> > > > > GROMACS is written by:
> > > > >  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> > > > > Bjelkmar
> > > > >  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
> > > > Groenhof
> > > > >  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> > > > > Karkoulis
> > > > > Peter KassonJiri Kraus  Carsten Kutzner  Per
> > > Larsson
> > > > >   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
> > > Marklund
> > > > >Teemu Murtola   Szilard Pall   Sander Pronk  Roland
> > > Schulz
> > > > >   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> > > > Tieleman
> > > > >   Teemu Virolainen  Christian WennbergMaarten Wolf
> > > > >and the project leaders:
> > > > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der
> > Spoel
> > > > >
> > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > > > > Copyright (c) 2001-2017, The GROMACS development team at
> > > > > Uppsala University, Stockholm University and
> > > > > the Royal Institute of Technology, Sweden.
> > > > > check out http://www.gromacs.org for more information.
> > > > >
> > > > > GROMACS is free software; you can redistribute it and/or modify it
> > > > > under the terms of the GNU Lesser General Public License
> > > > > as published by the Free Software Foundation; either version 2.1
> > > > > of the License, or (at your option) any later version.
> > > > >
> > > > > GROMACS:  gmx mdrun, version 2016.5
> > > > > Executable:   /usr/local/gromacs/bin/gmx
> > > > > Data prefix:  /usr/local/gromacs
> > > > > Working dir:  /home/nitttr/Desktop/Hydroxy_chloroquine
> > > > > Command line:
> > > > >   gmx mdrun -v -deffnm em
> > > > >
> > > > >
> > > > > Back Off! I just backed up em.log to ./#em.log.7#
> > > > >
> > > > > Running on 1 node with total 16 cores, 32 logical cores, 1
> compatible
> > > GPU
> > > > > Hardware detected:
> > > > >   CPU info:
> > > > > Vendor: Intel
> > > > > Brand:  Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
> > > > > SIMD instructions most likely to fit this hardware: AVX_512
> > > > > SIMD instructions selected at GROMACS compile time: AVX_512
> > > > >
> > > > >   Hardware topology: Basic
> > > > >   GPU info:
> > > > > Number of GPUs detected: 1
> > > > > #0: NVIDIA Tesla P4, compute cap.: 6.1, 

[gmx-users] Problem to build an infinite DNA chain ...

[Sergio Garay]

Hi all

I'm trying to build an infinite single DNA chain (all-atom AMBER bsc1 FF),
following a couple of old mails about this topic:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106130.html

But I have not achieved using pdb2gmx tool. I prepared my DNA with an extra
phosphate at the 5' terminal (As if this residue were inside the chain).
The number and order of the atoms is the same as the topology. Finally I
commented out all the entrance in dna.r2b file to force pdb2gmx to not make
any replacement at the terminal residues. But it still complains about the
terminals:


*Fatal error:There is a dangling bond at at least one of the terminal ends
and the force field does not provide terminal entries or files. Fix your
terminal residues so that they match the residue database (.rtp) entries,
or provide terminal database entries (.tdb).*

But there isn't any dangling bond in my molecule: the atoms in my pdb file
match perfectly with the ones in the dna.rtp file.

Can anyone give me a good clue to manage this problem? Is it possible? I
did not find any DNA simulation which treats DNA as a periodic molecule (or
may be, some of you can give any cite obout this kind of problems).

Thank you very much in advance!
Sergio
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[gmx-users] Gromacs /MMPBSA Calculation

[Navneet Kumar Singh]

Hello Gromacs Developers/ Users

Which tool you use to calculate binding free energy for the trajectory file
obtained from gromacs ?I have used g_mmpbsa (
https://rashmikumari.github.io/g_mmpbsa), but at many instances it gives
either positive or high negative binding energy which makes difficult any
sort of comparison. Solute dielectric constant is said to be a variable
which is responsible for this error. Suggestions/solutions please.
-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
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Re: [gmx-users] regarding changing the scale from ps to ns

[sudha bhagwati]

Thanks for the reply.
But it did not work for me. Can you please write the command line, it would
be much helpful.
Thank you.

On Thu, Aug 29, 2019 at 2:33 PM Mohammadreza Niknam Hamidabad <
jj700phys...@gmail.com> wrote:

> Hi,
> I'm currently using Gromacs 2018 and I'm not quite sure about the 5.x
> version. The gyrate module doesn't have -tu flag so my suggestion is that
> you convert your .xtc file to a new xtc file with trjconv -tu ns then use
> gyrate for your calculation.
> I hope you find it useful.
>
> Best regards,
> Reza
>
>
> On Thu, Aug 29, 2019 at 7:38 AM sudha bhagwati 
> wrote:
>
>> Hi,
>>
>> I am using the GROAMCS 5.1.4 version.
>>
>> 
>> Running the commands below:
>>
>>
>> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
>> *OR*
>> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
>>
>>
>> Error while executing commands:
>>
>> *Error in user input:*
>>
>> *Invalid command-line optionsUnknown command-line option -tu*
>>
>> 
>>
>> I want to generate my plots for nanosecond scale. Could you please help me
>> out with this issue. I'd be really grateful to you.
>>
>> Thank you.
>>
>>
>> --
>> Thanks & regards
>> ~
>> Sudha Bhagwati
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>

-- 
Thanks & regards
~
Sudha Bhagwati
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Re: [gmx-users] regarding changing the scale from ps to ns

[Mohammadreza Niknam Hamidabad]

Hi,
I'm currently using Gromacs 2018 and I'm not quite sure about the 5.x
version. The gyrate module doesn't have -tu flag so my suggestion is that
you convert your .xtc file to a new xtc file with trjconv -tu ns then use
gyrate for your calculation.
I hope you find it useful.

Best regards,
Reza


On Thu, Aug 29, 2019 at 7:38 AM sudha bhagwati 
wrote:

> Hi,
>
> I am using the GROAMCS 5.1.4 version.
>
> 
> Running the commands below:
>
>
> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
> *OR*
> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
>
>
> Error while executing commands:
>
> *Error in user input:*
>
> *Invalid command-line optionsUnknown command-line option -tu*
>
> 
>
> I want to generate my plots for nanosecond scale. Could you please help me
> out with this issue. I'd be really grateful to you.
>
> Thank you.
>
>
> --
> Thanks & regards
> ~
> Sudha Bhagwati
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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