[gmx-users] about the output of g_density

[ibrahim khalil]

Dear GROMACS users,

I am simulating a graphene sheet in gromacs. I was trying to use the
g_density function to determine the density of distribution of carbon atoms
along the z axis.
I used the following line-

g_density -f traj.xtc -o density.xvg -n index.ndx -d Z

The sheet is placed in the XY plane, so g_density gives me a peak at a
certain z co-ordinate (which is okay).

But i have a problem with the value of the density. My box size is 100 nm x
100 nm x 100 nm and there is 16502 carbon atoms. As all the carbon atoms
are placed in a certain Z value-

my density should be equal to *(16502 x 1.99e-26 x e27)/ (100 x 100 x 100) *=
0.328 kg/m^3

(Assuming, mass of carbon atom = 1.99e-26 kg)

But g_density is giving me a value of 16.454.

I notice if i multiply 0.328 by 50 I get just about 16.454 and there are 50
points in the density.xvg file. Does it mean I have to divdie the result by
50 to get the correct result?

Am I making any mistake here?

Thanks in advance.
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Re: [gmx-users] Nvt T-coupling error

[Justin Lemkul]

On 1/6/16 11:07 AM, Poncho Arvayo Zatarain wrote:








I`m
running a simulation of dppe+dppe+ligand+wáter and i`m building
index with the command gmc make_ndx –f minimiz-gro –o index.ndx.
When i use the command the following options appears to build the
index:
0
System27592 atoms
1
Other  27592 atoms
2
LIG
 8 atoms
3
DPPC  8320 atoms
4
DPPE  7744 atoms
5
TIP3  11520 atoms




And
i selected 3|
4 | 2 | 5 and creates the group DPPC_DPPE_LIG_TIP3
with 27592 atoms. Then i used the command instruction gmx
grompp -f nvt.mdp -c minimiz.gro -p dppc+dppe+ligand+water.top -n
index.ndx -o nvt.tpr, i run it and the following error appears:


Well:


Fatal error: 11520 atoms are not part of any of the T-coupling groups.


This is a clue:

5 TIP3  11520 atoms

and:

tc-grps = DPPC DPPELIG

So there's your problem.

-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] Nvt T-coupling error

[Poncho Arvayo Zatarain]

I`m
running a simulation of dppe+dppe+ligand+wáter and i`m building
index with the command gmc make_ndx –f minimiz-gro –o index.ndx.
When i use the command the following options appears to build the
index:
0
System27592 atoms
1
Other  27592 atoms
2
LIG
8 atoms
3
DPPC  8320 atoms
4
DPPE  7744 atoms
5
TIP3  11520 atoms




And
i selected 3|
4 | 2 | 5 and creates the group DPPC_DPPE_LIG_TIP3
with 27592 atoms. Then i used the command instruction gmx
grompp -f nvt.mdp -c minimiz.gro -p dppc+dppe+ligand+water.top -n
index.ndx -o nvt.tpr, i run it and the following error appears: Fatal
error: 11520 atoms are not part of any of the T-coupling groups. Could anybody 
help me to solve the error please? My nvt.mdp is the following:
title   = NVT equilibration for DPPC-DPPE-LIGANDdefine  = 
-DPOSRES  ; position restrain the protein; Run parametersintegrator   = 
md; leap-frog integratornsteps= 5 ; 2 * 
5 = 100 psdt  = 0.002 ; 2 fs; Output controlnstxout 
  = 100   ; save coordinates every 0.2 psnstvout  = 100 
  ; save velocities every 0.2 psnstenergy = 100   ; save 
energies every 0.2 psnstlog  = 100   ; update log file 
every 0.2 ps; Bond parameterscontinuation = no; first 
dynamics runconstraint_algorithm = lincs; holonomic constraints constraints 
= all-bonds ; all bonds (even heavy atom-H bonds) 
constrainedlincs_iter = 1 ; accuracy of 
LINCSlincs_order  = 4 ; also related to accuracy; 
Neighborsearchingns_type= grid  ; search neighboring 
grid celsnstlist   = 5 ; 10 fsrlist= 
1.2   ; short-range neighborlist cutoff (in nm)rcoulomb   = 1.2 
  ; short-range electrostatic cutoff (in nm)rvdw  = 1.2   ; 
short-range van der Waals cutoff (in nm); Electrostaticscoulombtype   = PME 
  ; Particle Mesh Ewald for long-range electrostaticspme_order= 4   
  ; cubic interpolationfourierspacing = 0.16  ; grid spacing 
for FFT; Temperature coupling is ontcoupl= V-rescale
 ; modified Berendsen thermostattc-grps  = DPPC DPPELIG 
 ; three coupling groups - more accuratetau_t= 0.1   0.1
 0.1 ; time constant, in psref_t = 303   303 303 ; 
reference temperature, one for each group, in K; Pressure coupling is offpcoupl 
  = no; no pressure coupling in NVT; Periodic boundary 
conditionspbc  = xyz   ; 3-D PBC; Dispersion 
correctionDispCorr= EnerPres  ; account for cut-off vdW scheme; 
Velocity generationgen_vel= yes   ; assign velocities from 
Maxwell distributiongen_temp   = 323   ; temperature for Maxwell 
distributiongen_seed  = -1; generate a random seed; COM motion 
removal; These options remove motion of the protein/bilayer relative to the 
solvent/ionsnstcomm= 1comm-mode= Linearcomm-grps   = 
DPPC_DPPE LIG   
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Re: [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

[Justin Lemkul]

On 1/6/16 1:20 AM, shagun krishna wrote:

Dear Gmx-user,

I am using LIE approach to calculate the binding energy of my protein and
ligand. When I am running g_lie program for my protein I am getting the
value of DeltaG= 0. Can you please suggest me a way to get the values of
Elj, Eqq, Clj and Cqq and also about the post-processing necessary to run a
LIE calculation. It is not given in tutorial. I have ran two separate
simulations: one for receptor-ligand complex and another for ligand alone
in solvent.  I am following Justin tutorial for free energy calculation.



For the sake of clarity in the archive, I again reiterate that my free energy 
tutorial has nothing to do with LIE.


The values of Elj and Eqq are what you get from simulating the ligand in water 
with appropriate energygrps.


The values of Clj and Cqq are the parameters you have to figure out.  What do 
the papers on LIE say?  There are defaults given in gmx lie, where do they come 
from?


-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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Re: [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

[shagun krishna]

Thanks for your reply Justin. I know it well that your that tutorial is
nothing to do with g_lie. But being as a gromacs user I am not getting this
point so I am asking this question.
For the protein I am taking all the default values which has been set by
g_lie program. And for the ligand we have to calculate it using g_energy
module. I have done with that part also. But f*or my ligand I am obtaining
Elj (LJ-14)= 226.365 and Eqq (*Coulomb-14) *= -125.048 (both in KJ/mol).**
When I am comparing them with their respective counterpart for the protein
(Clj and Cqq value 0.181 and 0.5 respectively; the Elj and Eqq values are
set 0 for the protein), they seem to be very large. Is it natural or there
is something wrong in my procedure. *
*PS I have performed simple gromacs simulation of ligand in water (that has
not included your free energy codes).*

*Regards*

*Shagun*

On Wed, Jan 6, 2016 at 9:42 PM, Justin Lemkul  wrote:

>
>
> On 1/6/16 1:20 AM, shagun krishna wrote:
>
>> Dear Gmx-user,
>>
>> I am using LIE approach to calculate the binding energy of my protein and
>> ligand. When I am running g_lie program for my protein I am getting the
>> value of DeltaG= 0. Can you please suggest me a way to get the values of
>> Elj, Eqq, Clj and Cqq and also about the post-processing necessary to run
>> a
>> LIE calculation. It is not given in tutorial. I have ran two separate
>> simulations: one for receptor-ligand complex and another for ligand alone
>> in solvent.  I am following Justin tutorial for free energy calculation.
>>
>>
> For the sake of clarity in the archive, I again reiterate that my free
> energy tutorial has nothing to do with LIE.
>
> The values of Elj and Eqq are what you get from simulating the ligand in
> water with appropriate energygrps.
>
> The values of Clj and Cqq are the parameters you have to figure out.  What
> do the papers on LIE say?  There are defaults given in gmx lie, where do
> they come from?
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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> posting!
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>
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Re: [gmx-users] Cannot write trajectory frame

[masoud keramati]

i just install the 64bit linux and problem solved :-)

On 1/4/16, masoud keramati  wrote:
> tnx dear Mark for your respond ;-)
> +
> Dear teemu
> yes my OS is 32-bit and version of gromacs is 5.x
> with installing 64bit OS, can i solve this problem?
>
> On Sun, Jan 3, 2016 at 6:53 PM, Teemu Murtola 
> wrote:
>
>> This is true, but unfortunately recent versions of Gromacs may not
>> properly
>> use the support present in 32-bit operating systems because of
>> http://redmine.gromacs.org/issues/1834.
>>
>> You haven't specified your Gromacs version or anything else about your
>> environment, so there is not much more we can guess.
>>
>> Best regards,
>> Teemu
>>
>> On Sun, Jan 3, 2016, 15:25 Mark Abraham  wrote:
>>
>> > Hi,
>> >
>> > Most modern file systems do not have such a limitation, and all modern
>> > operating systems support at least one of them, so all you need to do
>> > is
>> > have disks formatted accordingly.
>> >
>> > Mark
>> >
>> > On Sun, Jan 3, 2016 at 1:22 PM masoud keramati <
>> keramati.ma3...@gmail.com>
>> > wrote:
>> >
>> > > yes that's true .. and i'm searching for a way to remove this
>> limitation
>> > > but ,what you mean by "get a real one" ?
>> > >
>> > > On Sun, Jan 3, 2016 at 2:02 PM, Mark Abraham
>> > > > >
>> > > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > As you've read in the archive, this depends solely on your file
>> system.
>> > > Get
>> > > > a real one! :-)
>> > > >
>> > > > Mark
>> > > >
>> > > > On Sun, 3 Jan 2016 11:17 masoud keramati
>> > > > 
>> > > > wrote:
>> > > >
>> > > > > Hello and happy new year!
>> > > > >
>> > > > > i have seen this issue in archive,
>> > > > > the problem is with .trr size that can not reach more than 2GB
>> > > > > and
>> i
>> > > > think
>> > > > > that is my problem too.
>> > > > > my question is ,can i write .trr file with another file name and
>> then
>> > > > > finally append them?
>> > > > > is it a true way?
>> > > > >
>> > > > >
>> > > > > tnx for your responding ;-)
>> > > > > --
>> > > > > 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.
>> > > > >
>> > > > --
>> > > > Gromacs Users mailing list
>> > > >
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>> > > >
>> > > --
>> > > Gromacs Users mailing list
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>> > >
>> > --
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[gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

[hubert santuz]

Hi everyone,

I am trying to install the last version of Gromacs (5.1.1) on our SGI 
cluster.
The mono-processor compilation went fine and now I would like to compile 
the mdrun MPI version with the SGI MPT (the MPI library of SGI) 2.09 
(and also 2.12)

Here the cmake command I used:

cmake .. -DGMX_GPU=OFF -DCMAKE_C_COMPILER=gcc 
-DCMAKE_INSTALL_PREFIX=/opt/apps/software/pkg/gcc-4.9.0/mpt-2.0.9/gromacs/5.1.1/single 

-DFFTWF_LIBRARY=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/lib/libfftw3f.so 
-DFFTWF_INCLUDE_DIR=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/include 
 -DGMX_MPI=ON -DMPI_C_INCLUDE_PATH=/opt/sgi/mpt/mpt-2.12/include 
-DMPI_C_LIBRARIES=/opt/sgi/mpt/mpt-2.12/lib/libmpi.so 
-DGMX_BUILD_MDRUN_ONLY=ON  -DBUILD_SHARED_LIBS=off



The configuration went fine but when I ran make, I have the following error:


service0:gromacs-5.1.1/build # make
[  0%] Generating baseversion-gen.c
Scanning dependencies of target libgromacs
[  0%] Building C object 
src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwlzh.c.o

[...]
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o
[  4%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o
In file included from 
/opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/domdec/domdec_setup.cpp:53:0:
/opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/legacyheaders/names.h:110:25: 
erreur: expected unqualified-id before string constant

 #define UNDEFINED   "UNDEFINED"
 ^
make[2]: *** 
[src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o] Erreur 1

make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Erreur 2
make: *** [all] Erreur 2

This is strange because, as I said, the mono-processor compilation went 
fine.

I tried to upgrade the MPT library (2.12) without success.
I tried Openmpi 1.8.1 and it succeed.
Is there a compatibility issue with MPT ? I would like to keep this 
library since I achieved better performance with it.


Thanks,
Hubert
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Re: [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

[Mark Abraham]

Hi,

I suspect MPT has a bug such that one of its headers defines UNDEFINED,
which it should not do. If so, you can change src/gromacs/legacyheaders/names.h
lines 110-1 to read

#define GMX_UNDEFINED   "UNDEFINED"
#define ENUM_NAME(e, max, names)  e) < 0) || ((e) >= (max))) ?
GMX_UNDEFINED : (names)[e])

and you should be fine. If so, please let us know, and please file a bug
report with SGI.

Mark

On Wed, Jan 6, 2016 at 5:33 PM hubert santuz 
wrote:

> Hi everyone,
>
> I am trying to install the last version of Gromacs (5.1.1) on our SGI
> cluster.
> The mono-processor compilation went fine and now I would like to compile
> the mdrun MPI version with the SGI MPT (the MPI library of SGI) 2.09
> (and also 2.12)
> Here the cmake command I used:
>
> cmake .. -DGMX_GPU=OFF -DCMAKE_C_COMPILER=gcc
>
> -DCMAKE_INSTALL_PREFIX=/opt/apps/software/pkg/gcc-4.9.0/mpt-2.0.9/gromacs/5.1.1/single
>
>
> -DFFTWF_LIBRARY=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/lib/libfftw3f.so
>
> -DFFTWF_INCLUDE_DIR=/opt/apps/software/pkg/gcc-4.9.0/fftw/3.3.3/single/include
>   -DGMX_MPI=ON -DMPI_C_INCLUDE_PATH=/opt/sgi/mpt/mpt-2.12/include
> -DMPI_C_LIBRARIES=/opt/sgi/mpt/mpt-2.12/lib/libmpi.so
> -DGMX_BUILD_MDRUN_ONLY=ON  -DBUILD_SHARED_LIBS=off
>
>
> The configuration went fine but when I ran make, I have the following
> error:
>
>
> service0:gromacs-5.1.1/build # make
> [  0%] Generating baseversion-gen.c
> Scanning dependencies of target libgromacs
> [  0%] Building C object
>
> src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwlzh.c.o
> [...]
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o
> [  4%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o
> In file included from
>
> /opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/domdec/domdec_setup.cpp:53:0:
>
> /opt/apps/software/src/gromacs/gromacs-5.1.1/src/gromacs/legacyheaders/names.h:110:25:
> erreur: expected unqualified-id before string constant
>   #define UNDEFINED   "UNDEFINED"
>   ^
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o] Erreur 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Erreur 2
> make: *** [all] Erreur 2
>
> This is strange because, as I said, the mono-processor compilation went
> fine.
> I tried to upgrade the MPT library (2.12) without success.
> I tried Openmpi 1.8.1 and it succeed.
> Is there a compatibility issue with MPT ? I would like to keep this
> library since I achieved better performance with it.
>
> Thanks,
> Hubert
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Re: [gmx-users] error using pdb2gmx

[Irem Altan]

Alright, thank you! Apologies to everyone for duplicate e-mails.

Best,
Irem

> On Jan 6, 2016, at 4:23 PM, Mark Abraham  wrote:
> 
> Sorry, maybe it's [molecules]. Chapter 5 is your best friend ;-)
> 
> Mark
> 
> On Wed, Jan 6, 2016 at 9:35 PM Irem Altan  wrote:
> 
>> Hi,
>> 
>> I have a .pdb file that I generated by creating three more copies of the
>> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
>> on it, but I get the following error:
>> 
>> Fatal error:
>> Residue 111 named CYS of a molecule in the input file was mapped
>> to an entry in the topology database, but the atom CA used in
>> that entry is not found in the input file. Perhaps your atom
>> and/or residue naming needs to be fixed.
>> 
>> What is weird is that there is no residue 111 that is a cysteine (residue
>> 111 is a phenylalanine). I had run MD simulations successfully on a single
>> copy of this protein before. pdb2gmx runs without an error when I use the
>> old .pdb file. What could be the problem?
>> 
>> Best,
>> Irem
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Re: [gmx-users] distance dependent energy

[Cuong Nguyen]

Hi Mark,

I manage to find the way to record the energy but have not figured it out
yet. I used the .mdp file as below:

title= Molecular dynamics simulation at 298K
cpp  = cpp
integrator   = md
dt   = 0.001
nsteps   = 2000 ; 20 ns
comm-mode= Linear
nstcomm  = 200
nstxout  = 2000 ;trajectory file
nstvout  = 2000 ; velocity file
nstfout  = 0
nstlog   = 300 ;log file
nstenergy= 300 ; energy file
nstxtcout= 300
nstlist  = 100
ns_type  = grid
pbc  = xyz
coulombtype  = pme
rlist= 1.3
rcoulomb = 1.3
vdw-type = Cut-off
rvdw = 1.3
Tcoupl   = Nose-Hoover; Berendsen ; no pcoupl = NVT?
nsttcouple   = 50; half nstlist
tc_grps  = System
tau_t= 2.0
ref_t= 298.15
gen_vel  = no
gen_seed = 94839
constraints  = All-bonds
constraint-algorithm = lincs

Do you have any links or tutorials for that?

Best regards,

Van



Cuong Van Nguyen (PhD Student)
Department of Chemical Engineering
Curtin University, Western Australia
Tel. (+61) 45 221 3981


On 2 October 2015 at 11:16, Cuong Nguyen  wrote:

> Thank you Mark and Erik,
> Van
>
>
> On Wednesday, 23 September 2015, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen  wrote:
>>
>> > Dear Gromacs users,
>> >
>> > I would like to work out the energy (total and kinetic) as a function of
>> > the distance from the center of mass of a droplet. However, using
>> g_energy
>> > just gave me the values as a function of time. Could anyone tell me the
>> way
>> > to get the distance dependent values?
>> >
>>
>> First, you'd have to record them. mdrun doesn't work by first evaluating a
>> giant matrix of per-anything energies, and then adding them up. You can
>> use
>> energy groups to break down the short-ranged non-bonded component of the
>> potential energy into intra- and inter-group terms, but you can only have
>> 256 of them, and only with the group scheme, and only if you're not
>> concerned about diffusion (or are prepared to use dynamic selections and
>> mdrun -rerun creatively). And the work you have to put in to get that out
>> is not really worth thinking about unless you know exactly what you're
>> going to learn from the result.
>>
>> Mark
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>
>
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>
>
> Cuong Van Nguyen (PhD Student)
> Department of Chemical Engineering
> Curtin University, Western Australia
> Tel. (+61) 45 221 3981
>
>
>
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[gmx-users] Launch hybrid MPI/openMP run on multiple nodes

[Chunlei ZHANG]

Dear GMX developers and users,

I have a cluster of 24 nodes, each having two 10-core intel CPUs.
Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl.

I can successfully run a simulation by using pure MPI (480 MPI processes).
But the performance is not good and the log file of mdrun suggests using
fewer MPI processes.
I try to launch 240 MPI processes, each using 2 openMP threads, by the
command:
mpirun -ppn 20 -np 240 gmx_mpi mdrun -ntomp 2

But only a fraction of the nodes are running mdrun and the log file says:

Number of logical cores detected (20) does not match the number reported by
OpenMP (1).
Consider setting the launch configuration manually!

Does anyone know how to solve this problem?
Thanks in advance.

Best,
Chunlei
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Re: [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

[shagun krishna]

Hiii Justin,

Thanks again for replying to my query. I just wanted to know your opinion
that while performing ligand alone simulation in water, is it correct to
just take the .mdp files from lysozyme tutorial and change accordingly
without changing any parameters like Bond parameter,Neighborsearching,
Electrostatics, Temperature coupling and pressure coupling. Or can we take
these setting (except md; because in md.mdp it is using sd integrator, how
ever in all other settings it is using md integrator) from the Solvation
free energy of ethanol tutorial by Sander Pronk

I am using nvery expensive settings, I guess that this may be a probable
reason for getting higher values of Elj and Eqq. Kindly let me know that
from where should I select a the .mdp setting for simulation of ligand in
water only, without going through free energy codes.

Thanks in advance.

Regards,

Shagun

On Wed, Jan 6, 2016 at 11:27 PM, Justin Lemkul  wrote:

>
>
> On 1/6/16 12:52 PM, shagun krishna wrote:
>
>> Thanks for your reply Justin. I know it well that your that tutorial is
>> nothing to do with g_lie. But being as a gromacs user I am not getting
>> this
>> point so I am asking this question.
>>
>
> I was pointing it out for clarity in the archive only; I know you
> understand this point, but when someone types in the right words to Google,
> they may get seriously confused by what they see :)
>
> For the protein I am taking all the default values which has been set by
>> g_lie program. And for the ligand we have to calculate it using g_energy
>> module. I have done with that part also. But f*or my ligand I am obtaining
>> Elj (LJ-14)= 226.365 and Eqq (*Coulomb-14) *= -125.048 (both in KJ/mol).**
>> When I am comparing them with their respective counterpart for the protein
>> (Clj and Cqq value 0.181 and 0.5 respectively; the Elj and Eqq values are
>> set 0 for the protein), they seem to be very large. Is it natural or there
>> is something wrong in my procedure. *
>>
>
> 1-4 interactions are intramolecular terms. These are not what you want.
>
> You need:
>
> (1) Protein-ligand interaction energy (from energygrps = Protein LIG) in
> the complex simulation. You pass this .edr file to gmx lie.  Of course, if
> water plays any role in the interaction of the protein, or it is partially
> hydrated in the binding site, the result you get will not be right.
> (2) Ligand-water interaction energy (from energygrps = LIG SOL) from a
> simulation of the ligand in water. You pass these values to -Eqq and -Elj
> to gmx lie.
>
> As for the -Clj and -Cqq values, I still don't know.  Hopefully someone
> who does will chime in with something useful.  But again, the primary
> literature (and there are a number of LIE papers, I'm just not well-versed
> in their details) should tell you everything you need.
>
> -Justin
>
> *PS I have performed simple gromacs simulation of ligand in water (that has
>> not included your free energy codes).*
>>
>> *Regards*
>>
>> *Shagun*
>>
>>
>> On Wed, Jan 6, 2016 at 9:42 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/6/16 1:20 AM, shagun krishna wrote:
>>>
>>> Dear Gmx-user,

 I am using LIE approach to calculate the binding energy of my protein
 and
 ligand. When I am running g_lie program for my protein I am getting the
 value of DeltaG= 0. Can you please suggest me a way to get the values of
 Elj, Eqq, Clj and Cqq and also about the post-processing necessary to
 run
 a
 LIE calculation. It is not given in tutorial. I have ran two separate
 simulations: one for receptor-ligand complex and another for ligand
 alone
 in solvent.  I am following Justin tutorial for free energy calculation.


 For the sake of clarity in the archive, I again reiterate that my free
>>> energy tutorial has nothing to do with LIE.
>>>
>>> The values of Elj and Eqq are what you get from simulating the ligand in
>>> water with appropriate energygrps.
>>>
>>> The values of Clj and Cqq are the parameters you have to figure out.
>>> What
>>> do the papers on LIE say?  There are defaults given in gmx lie, where do
>>> they come from?
>>>
>>> -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
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
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>>> posting!
>>>
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>>>
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>>> 

[gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

Hi all,

I thought I would try using the -membed option of mdrun to insert a
helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions on
g_membed to generate my required .tpr file. Upon calling grommp I get:

ERROR 1 [file membed_NPT.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme


My input file can be seen below. If seems as though the Integrator is the
issue, even though I¹ve picked the correct one. Is a place holder feature?

Many thanks
Anthony

integrator = md
energygrps = Protein
freezegrps = Protein
freezedim = Y Y Y
energygrp_excl = Protein Protein


nsteps  = 500   ; 2 * 50 = 1000 ps (2 ns)
dt  = 0.002 ; 2 fs
nstxout = 1 ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
nstenergy   = 1 ; save energies every 0.2 ps
nstlog  = 1 ; update log file every 0.2 ps

continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)

coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

tcoupl  = Berendsen   ;Nose-Hoover  ; More
accurate thermostat
tc-grps = Protein  POPC SOL ; three coupling groups - more
accurate
tau_t   = 0.5   0.5 0.5 ; time constant, in ps
ref_t   = 310   310 310 ; reference temperature,
one for each group, in K

pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box
vectors, independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y,
z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility,
bar^-1

pbc = xyz   ; 3-D PBC
DispCorr= EnerPres  ; account for cut-off vdW scheme
gen_vel = no; Velocity generation is off
nstcomm = 1
comm-mode   = Linear
comm-grps   = POPC_Protein SOL
refcoord_scaling = com


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Re: [gmx-users] membed in mdrun VERSION 5.0.4

[Justin Lemkul]

On 1/6/16 2:00 PM, Nash, Anthony wrote:

Hi all,

I thought I would try using the -membed option of mdrun to insert a
helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions on
g_membed to generate my required .tpr file. Upon calling grommp I get:

ERROR 1 [file membed_NPT.mdp]:
   Energy group exclusions are not (yet) implemented for the Verlet scheme


My input file can be seen below. If seems as though the Integrator is the
issue, even though I¹ve picked the correct one. Is a place holder feature?



It's not the integrator that's the problem.  It is, as the error states, the use 
of the Verlet cutoff scheme.  Presumably "cutoff-scheme = group" would 
circumvent this issue.


-Justin


Many thanks
Anthony

integrator = md
energygrps = Protein
freezegrps = Protein
freezedim = Y Y Y
energygrp_excl = Protein Protein


nsteps  = 500   ; 2 * 50 = 1000 ps (2 ns)
dt  = 0.002 ; 2 fs
nstxout = 1 ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
nstenergy   = 1 ; save energies every 0.2 ps
nstlog  = 1 ; update log file every 0.2 ps

continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)

coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

tcoupl  = Berendsen   ;Nose-Hoover  ; More
accurate thermostat
tc-grps = Protein  POPC SOL ; three coupling groups - more
accurate
tau_t   = 0.5   0.5 0.5 ; time constant, in ps
ref_t   = 310   310 310 ; reference temperature,
one for each group, in K

pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box
vectors, independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y,
z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility,
bar^-1

pbc = xyz   ; 3-D PBC
DispCorr= EnerPres  ; account for cut-off vdW scheme
gen_vel = no; Velocity generation is off
nstcomm = 1
comm-mode   = Linear
comm-grps   = POPC_Protein SOL
refcoord_scaling = com




--
==

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] error using pdb2gmx

[Irem Altan]

Hi,

I have a .pdb file that I generated by creating three more copies of the 
protein according to its P212121 symmetry. I am now trying to run pdb2gmx on 
it, but I get the following error:

Fatal error:
Residue 111 named CYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

What is weird is that there is no residue 111 that is a cysteine (residue 111 
is a phenylalanine). I had run MD simulations successfully on a single copy of 
this protein before. pdb2gmx runs without an error when I use the old .pdb 
file. What could be the problem?

Best,
Irem
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[gmx-users] error using pdb2gmx

[Irem Altan]

Hi,

I have a .pdb file that I generated by creating three more copies of the 
protein according to its P212121 symmetry. I am now trying to run pdb2gmx on 
it, but I get the following error:

Fatal error:
Residue 111 named CYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

What is weird is that there is no residue 111 that is a cysteine (residue 111 
is a phenylalanine). I had run MD simulations successfully on a single copy of 
this protein before. pdb2gmx runs without an error when I use the old .pdb 
file. What could be the problem?

Best,
Irem
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Re: [gmx-users] error using pdb2gmx

[Mark Abraham]

Hi,

You don't need to run pdb2gmx to generate copies, just edit the [system]
field of your topology to match your coordinate file.

Mark

On Wed, Jan 6, 2016 at 8:38 PM Irem Altan  wrote:

> Hi,
>
> I have a .pdb file that I generated by creating three more copies of the
> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
> on it, but I get the following error:
>
> Fatal error:
> Residue 111 named CYS of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CA used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> What is weird is that there is no residue 111 that is a cysteine (residue
> 111 is a phenylalanine). I had run MD simulations successfully on a single
> copy of this protein before. pdb2gmx runs without an error when I use the
> old .pdb file. What could be the problem?
>
> Best,
> Irem
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>
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Re: [gmx-users] error using pdb2gmx

[Mark Abraham]

Sorry, maybe it's [molecules]. Chapter 5 is your best friend ;-)

Mark

On Wed, Jan 6, 2016 at 9:35 PM Irem Altan  wrote:

> Hi,
>
> I have a .pdb file that I generated by creating three more copies of the
> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
> on it, but I get the following error:
>
> Fatal error:
> Residue 111 named CYS of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CA used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> What is weird is that there is no residue 111 that is a cysteine (residue
> 111 is a phenylalanine). I had run MD simulations successfully on a single
> copy of this protein before. pdb2gmx runs without an error when I use the
> old .pdb file. What could be the problem?
>
> Best,
> Irem
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>
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