Re: [gmx-users] energy minization mdp

[Justin Lemkul]

On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote:

Dear User

I have protein-ligand system. I have basic idea for energy minimization.mdp
parameter.
;
integrator = steep
emtol = 10.0
emstep = 0.01
nsteps = 500
energygrps = Protein OAI
;
nstlist= 1
cutoff-scheme = Verlet
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.0
pbc= xyz

but I have not idea how to write the parameter *where all the backbone
heavy atoms of the protein have to be constrained with an elastic constant
of 50 kcal /mol Å -2 and the other atoms should be free.*

Does anyone know how to write elastic constant parameter in energy
minimization mdp file.



Restraints are a topological construct, not one that is (directly) specified in 
the .mdp file.  Run your protein coordinates (only) through gmx genrestr and 
choose the backbone as the output group.  Specify the desired force constant on 
the command line (make sure to convert your value to kJ mol^-1 nm^-2).  Save the 
new position restraint file to something like "posre_bb.itp" and #include it in 
the topology in the protein's [moleculetype] section, e.g.


#ifdef POSRES_BB
#include "posre_bb.itp"
#endif

Then specify "define = -DPOSRES_BB" in the .mdp file.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] TIP4P-D Water itp file

[atanu das]

Hi All,
Does anyone have the itp file for TIP4P-D water (J. Phys. Chem. B, 2015, 119 
(16), pp 5113–5123) and also the parameters that are needed to be added to the 
ffnonbonded.itp file for this water model? 
ThanksAtanu
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Re: [gmx-users] About the QM/MM MD of Gromacs

[Clinton King]

In case anyone is interested, here is a copy of the script I am currently
using to interface Gromacs 2016.1 with Gaussian 09 without altering the
source code of Gaussian 09. It is based on Gerrit Groenhoef's script,
available at wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian, with some
alterations so that it better fits my particular system. One note, since I
use custom basis sets with Gaussian 09, this script requires that I include
a file in the job submission with the extension .basis so that the basis
set information is concatenated to the end of the job file that gets
submitted to Gaussian.

The supercomputer at our institution uses slurm for job submission, and I
set the following variables in my slurm job submisstion script:

export OMP_NUM_THREADS=1
export Data_prefix=/fslhome/crk9/gromacs/gromacs-2016.1/bin/gmx_mpi   #
location of Gromacs 2016.1 executable
export GMX_QM_GAUSS_EXE=gau
export GMX_QM_GAUSS_DIR=/fslhome/crk9/gromacs/   # the location of gau
export GMX_QM_GAUSSIAN_NCPUS=16
export GMX_QM_GAUSSIAN_MEMORY=2 # part of a workaround, since I couldn't
figure out how to tell gromacs that I wanted to give gaussian 16 GB of
memory to use
export QM_METHOD=M06
export QM_MEM=16gb
export QM_PROC=16


*start of script:*

#!/bin/bash
#
# Please read this carefully, you may need to change it on a few locations
#
# wrapper to call gaussian, convert in- and output with some (tedious)
# awk scripting into the 'old' formats and perform the call to the
# standard g09/g03 installed on the system.  For reasons I don't
# understand the system() routine does not like long filenames. I
# therefore call this script gau
#
# To make gromacs aware of this script, use GAUSS_EXE:
#
# export GMX_QM_GAUSS_EXE=
#
# Also make sure that gromacs can find it by using the full path
# location to this file:
#
# export GMX_QM_GAUSS_DIR=
#

#the next three lines are to include variables to fix the qm method and the
memory for gaussian, also a log file is generated to help track what's
going on in the qm #computations
echo "qm method is $QM_METHOD" >> QM.stats.log
echo "amount of memory for gaussian is $QM_MEM" >> QM.stats.log
echo "number of processors is $QM_PROC" >> QM.stats.log

# let gromacs write a "normal" gaussian input file, using the keyword
# determined by the User's input. Alternatively, it is possible now to
# provide different keywords by placing a header.com in the
# directory. This will take precedence over the gromacs keywords.

echo
'*' >>
QM.stats.log
echo 'new run' >> QM.stats.log

if [ -e QM.step ]
then
step=$(head -n 1 QM.step)
#echo "$step =>" >> QM.stats.log
[[ "$step" =~ ([0-9]+)$ ]] && step="$((BASH_REMATCH[1] + 1))";
#echo "$step" >> QM.stats.log
echo "Current step = $step" >> QM.stats.log
else
step=0
fi

echo $step > QM.step
# create some temporary files
if [ -e temp.com ]
then
rm -fr temp.com
echo 'removed temp file' >> QM.stats.log
else
echo 'temp file does not exist' >> QM.stats.log
fi

# The user has provide an own header.com with keywords, including the
title, but no whiteline after that!
if [ -e "$JOBNAME".com ]
then
cat "$JOBNAME".com >> temp.com
echo 'jobname = '>> "$JOBNAME" >> QM.stats.log
echo 'jobname.com exists, copied it to temp.com' >> QM.stats.log
else

# Use the gromacs keywords based on input in the mdp file
echo 'input.com---'>>QM.stats.log
cat input.com >> QM.stats.log
echo ''>>QM.stats.log
echo "%nprocshared=$QM_PROC" >> temp.com
awk -v w=0 '{if ( ( w == 0 ) && ( $1 != "%subst" )) print}{ if ($1 == "#P"
|| $1 == "#T") w=1}' input.com >> temp.com
echo "Nosymm units=bohr FORCE Punch=(Derivatives) iop(3/33=1)
Prop=(Field,Read) pseudo geom=nocrowd" >> temp.com
echo " " >> temp.com
echo "empty title" >> temp.com
echo "jobname = $JOBNAME" >> QM.stats.log
echo 'jobname.com exists, copied it to temp.com' >> QM.stats.log
fi

# Use the knowledge on the input structure to extract the coordinates, etc.
awk -v w=0 '{if (w == 1) print}{if ( $1 == "input-file") w=1}' input.com >>
temp.com
echo 'coordinates extracted' >> QM.stats.log

# The following section will add basis set information necessary when using
the 'gen' keyword
if [ -e "$JOBNAME".basis ]
then
cat "$JOBNAME".basis >> temp.com
echo 'basis exists and copied to temp.com' >> QM.stats.log
else
echo 'basis does not exist' >> QM.stats.log
fi

# IN order to get the gradients on the MM point charges, we request
# gaussian to compute the electrostatic gradients on these centers. We
# thus need to provide the coordinates of the nearby MM charges once more.
We
# again use our knowledge of the input structure and simply wait until
# we have read in four whitelines, which means we have arrived at the
# point charges field.
# Note that gaussian ALWAYS requires these positions to be in angstrom,
# even if units=bohr!
awk -v nlines=0 '{if (nlines == 4 && $1) printf 

[gmx-users] energy minization mdp

[Mohammad Zahidul Hossain Khan]

Dear User

I have protein-ligand system. I have basic idea for energy minimization.mdp
parameter.
;
integrator = steep
emtol = 10.0
emstep = 0.01
nsteps = 500
energygrps = Protein OAI
;
nstlist= 1
cutoff-scheme = Verlet
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.0
pbc= xyz

but I have not idea how to write the parameter *where all the backbone
heavy atoms of the protein have to be constrained with an elastic constant
of 50 kcal /mol Å -2 and the other atoms should be free.*

Does anyone know how to write elastic constant parameter in energy
minimization mdp file.

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] error message: Invalid transform ...

[Mark Abraham]

Hi,

The QM/MM code is essentially untested and unmaintained and wasn't
developed for that version of GAUSSIAN, so you're dicing with death. Death
looks like he's rolling well. ;-) I recommend using either the exact
software versions used in published work, or some other package.

Mark

On Fri, 28 Jul 2017 17:52 Clinton King  wrote:

> No, I haven't been changing the code. I have been doing mixed qm/mm (using
> Gaussian 09 for the qm calculations) with some frozen atoms in the qm
> region. There were two changes I made to this run that altered it from
> previously successful runs: I increased the time step slightly, and I added
> a gaussian keyword to allow the gaussian computation steps to tolerate
> close interatomic distances. I will continue to troubleshoot and send an
> update post if I learn any more about what might have caused this error
> message.
>
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
>
>
> > Message: 2
> > Date: Fri, 28 Jul 2017 07:10:57 +
> > From: Mark Abraham 
> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] error message: Invalid transform ...
> > Message-ID:
> > 

Re: [gmx-users] concatenate 2 trajectory files

[Mark Abraham]

Hi,

On Fri, 28 Jul 2017 17:49 Atila Petrosian  wrote:

> Dear gromacs users,
>
> I had done a md simulation for 100 ns. I continued that for another 50 ns.
>
> gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx
> gmx mdrun -nb gpu -v -deffnm 100
>
> gmx grompp -f 50.mdp -c 100.gro -p system.top -o 50.tpr -n index.ndx
> gmx mdrun -nb gpu -v -deffnm 50
>
> I concatenated these 2 trajectories (100.xtc and 50.xtc) using
>
> gmx trjcat -f 100.xtc 50.xtc -o 150.xtc -settime
>

Seems like you should simply use

gmx mdrun -s 100
gmx convert-tpr -f 100 -o 150 -extend 50
gmx mdrun -s 150 -cpi

and let the automated appending work for you, rather than you fussing with
getting filenames and -settime right. The latter does not scale well.

I want to know for analysis on final trajectory (150.xtc), which of
> tpr files is appropriate (100.tpr or 50.tpr)?


Depends on your analysis. They differ only in the contained configuration,
and the number of steps, so you decide. Generally, it's irrelevant.

Should I concatenate
> tpr files?
>

What would that even mean?

Mark

Best,
> Atila
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Re: [gmx-users] error message: Invalid transform ...

[Clinton King]

No, I haven't been changing the code. I have been doing mixed qm/mm (using
Gaussian 09 for the qm calculations) with some frozen atoms in the qm
region. There were two changes I made to this run that altered it from
previously successful runs: I increased the time step slightly, and I added
a gaussian keyword to allow the gaussian computation steps to tolerate
close interatomic distances. I will continue to troubleshoot and send an
update post if I learn any more about what might have caused this error
message.

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University


> Message: 2
> Date: Fri, 28 Jul 2017 07:10:57 +
> From: Mark Abraham 
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] error message: Invalid transform ...
> Message-ID:
> 

[gmx-users] concatenate 2 trajectory files

[Atila Petrosian]

Dear gromacs users,

I had done a md simulation for 100 ns. I continued that for another 50 ns.

gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx
gmx mdrun -nb gpu -v -deffnm 100

gmx grompp -f 50.mdp -c 100.gro -p system.top -o 50.tpr -n index.ndx
gmx mdrun -nb gpu -v -deffnm 50

I concatenated these 2 trajectories (100.xtc and 50.xtc) using

gmx trjcat -f 100.xtc 50.xtc -o 150.xtc -settime

I want to know for analysis on final trajectory (150.xtc), which of
tpr files is appropriate (100.tpr or 50.tpr)? Should I concatenate
tpr files?

Best,
Atila
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[gmx-users] On the modeling of a shear flow

[Gleb Novikov]

Dear GROMACS Users,
I am interesting in the work-flow of the shear flow modeling in GROMACS. 
 I am dealing with a complex MARTINI CG membrane system consisted of several 
proteins embedded within big POPC-cholesterol bi-layer solvated in 
non-polarizable water. Within this system I would like to introduce a shear 
flow in form of a force gradient acting in a specific direction along the X or 
Y plane resulting in a directed  acceleration of water on the surface of the 
membrane, thus mimicking a flow.
 I will be grateful for any ideas how this could be modeled in Gromacs e.g 
special setups for Barostats or more complex cases using steered codes of 
GROMACS?
Thanks in advance!
Gleb

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[gmx-users] How to define (or modify) a new potential function in Gromacs?

[lan hoa Trinh]

Dear Gromacs community,
I am attemping to use Gromacs for a Coarse - grained simulation. In our
model, we have a term similar to the angle harmonic potential term, but the
variable is not angle but the volume created by three consecutive vectors.
I don't know if there is a way to implement that kind of potential in
Gromacs?
I am looking forward to hearing from you.
Thank you very much in advanced,
Best regards,
*Lan Hoa*
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[gmx-users] ATOMTYPES directive

[lan hoa Trinh]

Dear Gromacs community,
In the [ atomtypes ] directive, according to Gromacs manual, it should have
7 seperated fields, which are name, at.num, mass, charge, ptype, c6, c12.
However, when I remove the field of at.num, Gromacs still works without
notifying any error. If I insert 2 fields more, it still doesn't notify
error. Only when I insert 3 fields more, it start notifying error.
I don't understand how Gromacs read through all the parameters and
determine what is c6, c12, etc...
I am looking forward to hearing from you.
Thank you very much in advance.
Best regards,
*Lan Hoa*
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Re: [gmx-users] gmx check

[Dawid das]

Thank you for explaining.

Best wishes,
Dawid

2017-07-28 15:11 GMT+02:00 Mark Abraham :

> Hi,
>
> Seems like the extremes of normal variation of unconstrained bonds. As gmx
> help check suggests, the feature exists as a quick sanity check. The use of
> "correct" is in the sense of "between sensible atom indices" rather than
> suggesting that only one length is valid.
>
> Mark
>
> On Fri, 28 Jul 2017 14:41 Dawid das  wrote:
>
> > Hi,
> >
> > No, those bonds I get the message were not constrained and virtually in
> > every frame there is different
> > bunch of bonds for which I get this message. Because the whole output
> from
> > gmx check is 1.1 GB,
> > I just give you a few examples.
> >
> > Reading frame   0 time0.000
> > # Atoms  24884
> > Precision 0.001 (nm)
> > Distance between atoms 53 and 55 is 0.149, should be 0.143
> > Distance between atoms 55 and 66 is 0.159, should be 0.149
> > Distance between atoms 70 and 81 is 0.155, should be 0.149
> > Distance between atoms 72 and 75 is 0.160, should be 0.153
> > Distance between atoms 102 and 104 is 0.152, should be 0.143
> > Distance between atoms 104 and 120 is 0.154, should be 0.149
> > .
> > .
> > .
> >
> > then
> >
> > Reading frame   1 time2.000   Distance between atoms 11 and 13 is
> > 0.139, should be 0.134
> > Distance between atoms 15 and 17 is 0.162, should be 0.154
> > Distance between atoms 26 and 28 is 0.148, should be 0.154
> > Distance between atoms 26 and 44 is 0.158, should be 0.149
> > Distance between atoms 31 and 34 is 0.147, should be 0.153
> > Distance between atoms 48 and 51 is 0.155, should be 0.149
> > Distance between atoms 51 and 53 is 0.129, should be 0.134
> > Distance between atoms 55 and 57 is 0.160, should be 0.154
> > Distance between atoms 55 and 66 is 0.154, should be 0.149
> > Distance between atoms 70 and 81 is 0.159, should be 0.149
> > Distance between atoms 78 and 79 is 0.121, should be 0.126
> > Distance between atoms 81 and 82 is 0.119, should be 0.123
> > .
> > .
> > .
> > and so on. What do you think about that?
> >
> > Best wishes,
> > Dawid
> >
> > 2017-07-28 13:33 GMT+02:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > It's hard to tell without seeing the messages and knowing whether those
> > > bonds were constrained.
> > >
> > > Mark
> > >
> > > On Fri, 28 Jul 2017 13:19 Dawid das  wrote:
> > >
> > > > Dear Gromacs Users,
> > > >
> > > > I get a bunch of communicates when I run
> > > > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
> > > >
> > > > saying that I get different bond lengths than they should be. Can
> that
> > be
> > > > caused by only 0.001 nm precision of my results?
> > > > Also I am not exactly sure if I understand correctly what I am
> checking
> > > > here.
> > > > "If both a trajectory and a .tpr <
> > > > http://manual.gromacs.org/online/tpr.html>
> > > > file are given (with -s1) the program will check whether the bond
> > lengths
> > > > defined in the tpr  file
> > are
> > > > indeed correct in the trajectory."
> > > > If so, then what does it mean "correct" in this sentence? It is
> pretty
> > > > obvious that
> > > > bond lengths vary during simulation unless I constrain them.
> > > >
> > > > Best wishes,
> > > > Dawid Grabarek
> > > > --
> > > > 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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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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> > >
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> 

Re: [gmx-users] gmx check

[Mark Abraham]

Hi,

Seems like the extremes of normal variation of unconstrained bonds. As gmx
help check suggests, the feature exists as a quick sanity check. The use of
"correct" is in the sense of "between sensible atom indices" rather than
suggesting that only one length is valid.

Mark

On Fri, 28 Jul 2017 14:41 Dawid das  wrote:

> Hi,
>
> No, those bonds I get the message were not constrained and virtually in
> every frame there is different
> bunch of bonds for which I get this message. Because the whole output from
> gmx check is 1.1 GB,
> I just give you a few examples.
>
> Reading frame   0 time0.000
> # Atoms  24884
> Precision 0.001 (nm)
> Distance between atoms 53 and 55 is 0.149, should be 0.143
> Distance between atoms 55 and 66 is 0.159, should be 0.149
> Distance between atoms 70 and 81 is 0.155, should be 0.149
> Distance between atoms 72 and 75 is 0.160, should be 0.153
> Distance between atoms 102 and 104 is 0.152, should be 0.143
> Distance between atoms 104 and 120 is 0.154, should be 0.149
> .
> .
> .
>
> then
>
> Reading frame   1 time2.000   Distance between atoms 11 and 13 is
> 0.139, should be 0.134
> Distance between atoms 15 and 17 is 0.162, should be 0.154
> Distance between atoms 26 and 28 is 0.148, should be 0.154
> Distance between atoms 26 and 44 is 0.158, should be 0.149
> Distance between atoms 31 and 34 is 0.147, should be 0.153
> Distance between atoms 48 and 51 is 0.155, should be 0.149
> Distance between atoms 51 and 53 is 0.129, should be 0.134
> Distance between atoms 55 and 57 is 0.160, should be 0.154
> Distance between atoms 55 and 66 is 0.154, should be 0.149
> Distance between atoms 70 and 81 is 0.159, should be 0.149
> Distance between atoms 78 and 79 is 0.121, should be 0.126
> Distance between atoms 81 and 82 is 0.119, should be 0.123
> .
> .
> .
> and so on. What do you think about that?
>
> Best wishes,
> Dawid
>
> 2017-07-28 13:33 GMT+02:00 Mark Abraham :
>
> > Hi,
> >
> > It's hard to tell without seeing the messages and knowing whether those
> > bonds were constrained.
> >
> > Mark
> >
> > On Fri, 28 Jul 2017 13:19 Dawid das  wrote:
> >
> > > Dear Gromacs Users,
> > >
> > > I get a bunch of communicates when I run
> > > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
> > >
> > > saying that I get different bond lengths than they should be. Can that
> be
> > > caused by only 0.001 nm precision of my results?
> > > Also I am not exactly sure if I understand correctly what I am checking
> > > here.
> > > "If both a trajectory and a .tpr <
> > > http://manual.gromacs.org/online/tpr.html>
> > > file are given (with -s1) the program will check whether the bond
> lengths
> > > defined in the tpr  file
> are
> > > indeed correct in the trajectory."
> > > If so, then what does it mean "correct" in this sentence? It is pretty
> > > obvious that
> > > bond lengths vary during simulation unless I constrain them.
> > >
> > > Best wishes,
> > > Dawid Grabarek
> > > --
> > > 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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Re: [gmx-users] gmx check

[Dawid das]

Hi,

No, those bonds I get the message were not constrained and virtually in
every frame there is different
bunch of bonds for which I get this message. Because the whole output from
gmx check is 1.1 GB,
I just give you a few examples.

Reading frame   0 time0.000
# Atoms  24884
Precision 0.001 (nm)
Distance between atoms 53 and 55 is 0.149, should be 0.143
Distance between atoms 55 and 66 is 0.159, should be 0.149
Distance between atoms 70 and 81 is 0.155, should be 0.149
Distance between atoms 72 and 75 is 0.160, should be 0.153
Distance between atoms 102 and 104 is 0.152, should be 0.143
Distance between atoms 104 and 120 is 0.154, should be 0.149
.
.
.

then

Reading frame   1 time2.000   Distance between atoms 11 and 13 is
0.139, should be 0.134
Distance between atoms 15 and 17 is 0.162, should be 0.154
Distance between atoms 26 and 28 is 0.148, should be 0.154
Distance between atoms 26 and 44 is 0.158, should be 0.149
Distance between atoms 31 and 34 is 0.147, should be 0.153
Distance between atoms 48 and 51 is 0.155, should be 0.149
Distance between atoms 51 and 53 is 0.129, should be 0.134
Distance between atoms 55 and 57 is 0.160, should be 0.154
Distance between atoms 55 and 66 is 0.154, should be 0.149
Distance between atoms 70 and 81 is 0.159, should be 0.149
Distance between atoms 78 and 79 is 0.121, should be 0.126
Distance between atoms 81 and 82 is 0.119, should be 0.123
.
.
.
and so on. What do you think about that?

Best wishes,
Dawid

2017-07-28 13:33 GMT+02:00 Mark Abraham :

> Hi,
>
> It's hard to tell without seeing the messages and knowing whether those
> bonds were constrained.
>
> Mark
>
> On Fri, 28 Jul 2017 13:19 Dawid das  wrote:
>
> > Dear Gromacs Users,
> >
> > I get a bunch of communicates when I run
> > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
> >
> > saying that I get different bond lengths than they should be. Can that be
> > caused by only 0.001 nm precision of my results?
> > Also I am not exactly sure if I understand correctly what I am checking
> > here.
> > "If both a trajectory and a .tpr <
> > http://manual.gromacs.org/online/tpr.html>
> > file are given (with -s1) the program will check whether the bond lengths
> > defined in the tpr  file are
> > indeed correct in the trajectory."
> > If so, then what does it mean "correct" in this sentence? It is pretty
> > obvious that
> > bond lengths vary during simulation unless I constrain them.
> >
> > Best wishes,
> > Dawid Grabarek
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] gmx check

[Mark Abraham]

Hi,

It's hard to tell without seeing the messages and knowing whether those
bonds were constrained.

Mark

On Fri, 28 Jul 2017 13:19 Dawid das  wrote:

> Dear Gromacs Users,
>
> I get a bunch of communicates when I run
> gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
>
> saying that I get different bond lengths than they should be. Can that be
> caused by only 0.001 nm precision of my results?
> Also I am not exactly sure if I understand correctly what I am checking
> here.
> "If both a trajectory and a .tpr <
> http://manual.gromacs.org/online/tpr.html>
> file are given (with -s1) the program will check whether the bond lengths
> defined in the tpr  file are
> indeed correct in the trajectory."
> If so, then what does it mean "correct" in this sentence? It is pretty
> obvious that
> bond lengths vary during simulation unless I constrain them.
>
> Best wishes,
> Dawid Grabarek
> --
> Gromacs Users mailing list
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[gmx-users] gmx check

[Dawid das]

Dear Gromacs Users,

I get a bunch of communicates when I run
gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out

saying that I get different bond lengths than they should be. Can that be
caused by only 0.001 nm precision of my results?
Also I am not exactly sure if I understand correctly what I am checking
here.
"If both a trajectory and a .tpr 
file are given (with -s1) the program will check whether the bond lengths
defined in the tpr  file are
indeed correct in the trajectory."
If so, then what does it mean "correct" in this sentence? It is pretty
obvious that
bond lengths vary during simulation unless I constrain them.

Best wishes,
Dawid Grabarek
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Re: [gmx-users] Using external force field with GROMACS

[Qinghua Liao]

Hello,

You can also set the variable of GMXLIB so that pdb2gmx can find the 
force field you want to use, like:

GMXLIB=/ path /charmm36m.ff


Best,
Qinghua

On 07/28/2017 10:53 AM, Souparno Adhikary wrote:

Hi,

I want to use the latest CHARMM36m force field which I downloaded from
MacKerell group's website. I use a common HPC system and do not have an
administrator account.

Can you give me an idea how I can add this forcefield to the pdb2gmx
options? We are using quite an old version of GROMACS- 4.5.6 (I don't know
why they are not eager to update it).

Thanks,

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.


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Re: [gmx-users] Using external force field with GROMACS

[David van der Spoel]

On 28/07/17 10:53, Souparno Adhikary wrote:

Hi,

I want to use the latest CHARMM36m force field which I downloaded from
MacKerell group's website. I use a common HPC system and do not have an
administrator account.

Can you give me an idea how I can add this forcefield to the pdb2gmx
options? We are using quite an old version of GROMACS- 4.5.6 (I don't know
why they are not eager to update it).

You can install gromacs yourself in your own directory. Start with that.



Thanks,

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Using external force field with GROMACS

[Mark Abraham]

Hi,

On Fri, 28 Jul 2017 10:53 Souparno Adhikary  wrote:

> Hi,
>
> I want to use the latest CHARMM36m force field which I downloaded from
> MacKerell group's website. I use a common HPC system and do not have an
> administrator account.
>
> Can you give me an idea how I can add this forcefield to the pdb2gmx
> options? We are using quite an old version of GROMACS- 4.5.6 (I don't know
> why they are not eager to update it).
>

The tools will find such force field folders when they are present in your
working directory also. I forget whether such ancient versions have support
for that.

If nobody asks for a recent version of GROMACS, sysadmins are busy people
and do other things with their time. Ask them ;-)

Mark


Thanks,
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
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Re: [gmx-users] How to increase the volatile gpu-util

[Mark Abraham]

Hi,

On Fri, 28 Jul 2017 10:37 leila karami  wrote:

> Dear gromacs users,
>
> I am running CG MD simulation on a Rocks cluster using the following
> command:
>
> gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job &
>
> I tried the different value for the -ntomp option. With -ntomp 16 run
> will finish sooner than the other values for -ntomp.
>
> In this state, volatile gpu-util is 47%. How to increase this parameter?
>

Much more relevant is what gromacs reports in the end of the log file.
Sharing a whole log file via a file sharing service is a useful way to get
some tips.

Mark

nvidia-smi command:
>
>
> |*---+--+--+
> *|* GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
> *ECC |
> |* Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
> *M. |
>
> |*===+==+==|
> *|*   2  TITAN X (Pascal)On   | :C1:00.0 Off |
> * N/A |
> |* 43%   71CP2   130W / 250W |183MiB / 12189MiB | 47%   E.
> *Process |
>
> +---+--+--+
>
> Any help will be highly appreciated.
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[gmx-users] Using external force field with GROMACS

[Souparno Adhikary]

Hi,

I want to use the latest CHARMM36m force field which I downloaded from
MacKerell group's website. I use a common HPC system and do not have an
administrator account.

Can you give me an idea how I can add this forcefield to the pdb2gmx
options? We are using quite an old version of GROMACS- 4.5.6 (I don't know
why they are not eager to update it).

Thanks,

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.
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[gmx-users] How to increase the volatile gpu-util

[leila karami]

Dear gromacs users,

I am running CG MD simulation on a Rocks cluster using the following
command:

gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job &

I tried the different value for the -ntomp option. With -ntomp 16 run
will finish sooner than the other values for -ntomp.

In this state, volatile gpu-util is 47%. How to increase this parameter?

nvidia-smi command:

|*---+--+--+
*|* GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
*ECC |
|* Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
*M. |
|*===+==+==|
*|*   2  TITAN X (Pascal)On   | :C1:00.0 Off |
* N/A |
|* 43%   71CP2   130W / 250W |183MiB / 12189MiB | 47%   E.
*Process |
+---+--+--+

Any help will be highly appreciated.
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Re: [gmx-users] Performance values

[Maureen Chew]

You might find this reference handy - it has a really nice explanation for how 
to look 
at a log file
Topology preparation, "What's in a log file", basic performance improvements: 
Mark Abraham, Session 1A 


The “Performance:” values are a throughput measure where both values represent
the same thing in different terms.  In your sample below, 3.964 is the
number of nanoseconds that can be simulated in 24 hours while it takes
6.054 hours to simulate 1 ns

HTH


On Jul 27, 2017, at 10:15 AM, Maureen Chew  wrote:
> Where is it documented how the mdrun performance metrics are calculated ? I?ve
> looked here
> http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html
>  
> 
> and here
> http://manual.gromacs.org/documentation/2016.3/manual-2016.3.pdf 
> 
> 
> but seem to have missed  explanation.  
> 
> Are the sample mdrun times below user time or real time?  Generally, wall is 
> real time
> I understand that ?Performance:? is not a linear scale but what is the scale
> in the 2016.3 sample below?
> 
>  Core t (s)   Wall t (s)(%)
>   Time:69761.050  272.50425600.0
> (ns/day)(hour/ns)
> Performance:3.9646.054
> 

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Re: [gmx-users] gmx complains of mismatch between index and trajectory file

[Mark Abraham]

Hi,

Your xtc file has only the group you wrote, so it isn't valid to index into
it with an index file that was made for a conformation with many other
atoms. That's the mismatch the message mentions. For your xtc, "System" is
the subset of *it* that you seem to want for your analysis. Note that gmx
convert-tpr -f topol.tpr -n -o subset.tpr is sometimes needed for giving an
analysis tool a matching coordinate and trajectory file. That would let you
then build eg a Protein group that was valid to index into your trajectory.

Mark

On Fri, 28 Jul 2017 01:46 Jared Sagendorf  wrote:

> Hello, I'm using GROMACS 5.1.13 and ran into a problem I've never
> encountered before. I've run a simulation on a zinc-finger DNA complex and
> defined a group in my index filed called "Protein_DNA" from the default
> "Protein" and "DNA" groups. This group should contain 4666 atoms, which it
> does.
>
> $gmx make_ndx -n index.ndx
> 0 System  : 180141 atoms
> 1 Protein :  2830 atoms <==
> 2 Protein-H   :  1427 atoms
> 3 C-alpha :   171 atoms
> 4 Backbone:   513 atoms
> 5 MainChain   :   685 atoms
> 6 MainChain+Cb:   851 atoms
> 7 MainChain+H :   854 atoms
> 8 SideChain   :  1976 atoms
> 9 SideChain-H :   742 atoms
> 10 Prot-Masses :  2830 atoms
> 11 non-Protein : 177311 atoms
> 12 Ion :32 atoms
> 13 ZN  : 7 atoms
> 14 NA  :25 atoms
> 15 DNA :  1836 atoms <=
> 16 ZN  : 7 atoms
> 17 NA  :25 atoms
> 18 Water   : 175443 atoms
> 19 SOL : 175443 atoms
> 20 non-Water   :  4698 atoms
> 21 Water_and_ions  : 175475 atoms
> 22 Protein_DNA :  4666 atoms <=
>
> I'm not sure why the ZN and NA groups show up twice, but I assume it's not
> an issue. Anyway, Protein_DNA is defined, and when I compare the values in
> the index.ndx file to the atom numbers in the .gro file, it all matches up.
>
> In my .mdp input file, I specify this group to be output as a compressed
> .xtc trajectory.
>
> ; OUTPUT CONTROL OPTIONS =
> nstxout  = 1
> nstvout  = 1
> nstfout  = 0
> nstlog   = 1
> nstenergy= 2500
> nstxout-compressed   = 1000
> compressed-x-precision   = 1000
> compressed-x-grps= Protein_DNA
>
> And then I run my simulation. I now have my traj.xtc file, which I want to
> process. However, when using gmx trjconv, and select the group Protein_DNA,
> I get the following error:
> $gmx trjconv -f traj.xtc -n index.ndx [options]
> Fatal error:
> Index[4659] 4667 is larger than the number of atoms in the
> trajectory file (4666). There is a mismatch in the contents
> of your -f, -s and/or -n files.
>
> The group DNA_Protein should contain 4666 atoms, and I've verified that my
> traj.xtc file indeed contains 4666 items with gmx check:
>
> $gmx check -f traj.xtc
> Checking file traj.xtc
> Reading frame   0 time0.000
> # Atoms  4666
> ...
>
> So what is the problem here? The error message states that "Index[4659]
> 4667 is larger than the number of atoms in the trajectory file (4666)",
> which is true - the 4659th atom listed in the "Protein_DNA" index is indeed
> atom 4667, but so what? There's 4666 atoms in the index, and 4666 atoms in
> traj.xtc file - I don't see where the mismatch is.
>
> Can someone help me out with this and suggest some things to try, or
> explain what is wrong if I'm missing something?
>
> Is it possible this is related to the fact that the protein topology file
> includes 7 zinc atoms (since this is a ZF protein), which are not included
> in the group Protein_DNA? Note that if I don't supply an index file and
> choose "Protein" from the default groups, gmx
> trjconv will run, but if I choose "DNA", I get a similar error.
>
> Fatal error:
> Index[1829] 4667 is larger than the number of atoms in the
> trajectory file (4666). There is a mismatch in the contents
> of your -f, -s and/or -n files.
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Re: [gmx-users] error message: Invalid transform ...

[Mark Abraham]

Hi,

That's a new one for me ;-) So new that I assume you were changing the code?

Mark

On Fri, 28 Jul 2017 00:51 Clinton King  wrote:

> Has anybody ever seen the following error message before?
>
>
> Program: gmx mdrun, version 2016.1
> Source file: src/gromacs/fft/parallel_3dfft.cpp (line 173)
>
> *Fatal error:*
> *Invalid transform. Plan and execution don't match regarding reel/complex*
>
>
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
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