[gmx-users] how to change the color scale on covariance matrix plots made with g_covar ?

[Evelyne Deplazes]

Hi guys

I am using g_covar to calculate the covariance matrix for 3 different
simulations systems. The commands I use are

echo "21 17" | ~/programs/gromacs/3.3.3/bin/g_covar -f
trajout_channel_allwindows.xtc  -s run_1.tpr -n index.ndx -o
eigenval_chABC_fitwithoutthumb_allwindows.xvg -l
covar_chABC_fitwithoutthumb_allwindows.log -xpma
covar_chABC_fitwithoutthumb_allwindows.xpm

xpm2ps -f covar_chABC_fitwithoutthumb_allwindows.xpm -o
covar_chABC_fitwithoutthumb_allwindows.eps


I then repeat the same thing for the two other systems so I end up with 3
.xpm and .eps files. The Problem is that the color range of the matrices.
They a) don't range from -X to +X (eg for one of them matrices it goes
from -1.2 to 2.92) and b) the range is different for each matrix. That
makes it very hard to compare them


How can I set the scale for the matrix either in g_covar? Or do have to
post-process the .xpm file? If so, how?

Thanks
Evelyne 



 
Dr. Evelyne Deplazes, PhD
NHMRC Early Career Fellow (Curtin University)
Visiting Academic, The University of Queensland
St. Lucia, QLD 4072, Australia
http://oasisapps.curtin.edu.au/staff/profile/view/Evelyne.Deplazes




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[gmx-users] Fwd: (no subject)

[Kingsley Theras Primus Dass .]

-- Forwarded message --
From: "Kingsley Theras Primus Dass ." <105726...@gms.tcu.edu.tw>
Date: 3 Nov 2016 11:42 a.m.
Subject: [gmx-users] (no subject)
To: 
Cc:

Hello users !

I want to Add SO3- to tyrosine residue  of my protein. I generated the
topology file for SO3- (TYS) residue using PRODRUG server and incorporated
that topology into my topology. I am using GROMACS45a3 force field . but
still when i try running pdb2gmx , it shows error.

could you please suggest some solution for it .


Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/resall.c,
line: 486

Fatal error:
in .rtp file in residue TYS at line:
 1 O 1  TYS   O 1   -0.682  15.9994




Thank you
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[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Hello users !

I want to Add SO3- to tyrosine residue  of my protein. I generated the
topology file for SO3- (TYS) residue using PRODRUG server and incorporated
that topology into my topology. I am using GROMACS45a3 force field . but
still when i try running pdb2gmx , it shows error.

could you please suggest some solution for it .


Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/resall.c,
line: 486

Fatal error:
in .rtp file in residue TYS at line:
 1 O 1  TYS   O 1   -0.682  15.9994




Thank you
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[gmx-users] Energy Minimization

[Mishelle Oña]

Hello

I have a question about energy minimization tool. I am modelling a polymer and 
I use a force field I have developed. I have run a EM and got positive values. 
Can you help me with this?

Best regards,

Mishelle
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Re: [gmx-users] qmmm

[Adamu, Aliyu]

Dear Gerrit,

I did as you suggested and realised it is orca related problem. thanks a lot 
for you help. it really mean a lot to me.

many thanks
Aliyu Adamu

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Groenhof, 
Gerrit [ggro...@gwdg.de]
Sent: Wednesday, November 2, 2016 8:03 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] qmmm

Looks more like an issue running orca than with gromacs and it seems that 
you're trying to run orca with mpi, but don't have an mpirun in your path. Can 
you run ORCA stand-alone with the input file generated with gromacs? If it is 
orca related, please contact Orca crew.

Best,

Gerrit



Message: 4
Date: Tue, 1 Nov 2016 23:38:04 +
From: "Adamu, Aliyu" 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] qmmm
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Dear Gerrit,

thanks a lot for your email. when i used "export BASENAME=topol" as you 
suggested, that particular error was solved. but yet i got another error 
reading as:

starting mdrun 'Protein'
5000 steps,  5.0 ps.
Calling '/home/birg/orca//orca topol.inp >> topol.out'
sh: 1: mpirun: not found
ORCA finished by error termination in ORCA_GTOInt
Segmentation fault (core dumped)

I dont know what is wrong, because i am running the calculation on just one PC

many thanks
Aliyu Adamu

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Groenhof, 
Gerrit [ggro...@gwdg.de]
Sent: Tuesday, November 1, 2016 12:45 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] qmmm

depending on the shell try using "export BASENAME=topol" or "setenv BASENAME 
topop' instead. You can check if things worked by typing echo $BASENAME which 
should be topol.

I am surprised you did not get an error message form the shell after typing 
these lines...

Gerrit

Message: 3
Date: Tue, 1 Nov 2016 10:57:07 +
From: "Adamu, Aliyu" 
To: "gmx-us...@gromacs.org" 
Subject: [gmx-users] qmmm
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Hello Justin

could you please help me out on how to get over this problem? I want to run 
QM/MM calculation in GROMACS 4.6.7 and ORCA version 3.03. before i run the 
mdrun command i set the environment variables: BASENAME and ORCA_PATH by typing 
the following command in the shell:

BASENAME=topol
ORCA_PATH=/home/birg/orca

But when i type the command for the mdrun as:

mdrun -v -c qmmm1out.gro

it gives me error massage that reads as:

---
Program mdrun, VERSION 4.6.7
Source code file: /home/birg/Downloads/gromacs-4.6.7/src/mdlib/qm_orca.c, line: 
86

Fatal error:
$BASENAME not set

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I dont know why is indicating basename not set. please help me out?

many thanks
Aliyu Adamu

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[gmx-users] Free energy profiles with Pull code : dimer/dimer interactions

[CROUZY Serge 119222]

Dear gromacs users

In previous mail on the list Justin argued about free energy calculations with 
Pull code that:
"For general
protein-ligand complexes, it is *NOT* appropriate to assume 
one-dimensional pulling or applying position restraints to the 
protein.  Our paper (from which the tutorial was derived) describes 
the somewhat unique case we were dealing with. "

 In my case, I'm calculating the profile for dimer dissociation in a 
 tetramer of proteins pulling on 1 dimer in direction X (because the 
tetramer is oriented in a such a way that X is the principal axis) 
while the other dimer is harmonically restrained (BB atoms only) 
I don't see how this could be done differently; although I'm hoping that 
 the free energy will result from the sole force between dimer/dimer 
 atoms: the restraint on one dimer should not affect the result .. As 
 long as they do not prevent the fluctuations (breathing) necessary for an 
almost reversible extraction of 
one dimer  from the tetramer. Is there a paper describing the possible effect 
of 
these restraints on the profile ?  (I suppose if one dimer is 
 completely fixed, the energy barrier for extraction will increase 
 dramatically because its residues won't be allowed to adjust while the 
 partner dimer is pulled out)

Thanks for your input

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux 
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110   
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT


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Re: [gmx-users] Orienting molecule in a correct direction

[Justin Lemkul]

On 11/1/16 11:22 AM, faride badalkhani wrote:

Hi,

You're right. I am sorry for the unclear explanation. I used the editconf
-princ command and chose ligand as the group for aligning in x direction.
then I used the editconf -rotate 0 90 0 to align along z. Then I executed
pdb2gmx command. Then
editconf -f complex.gro -o complex-box.gro -center 4 4 4 -box 8 8 24
I want to pull a total distance of 16 nm.


That's not possible with a box that size, unless you use geometry = 
direction_periodic, disable pressure coupling along z, and adjust other pull 
settings accordingly.  The maximum that you can pull in the z-dimension is 12 nm 
with these settings.




I continued the procedure till generating configurations and this is the
mdp file for pulling:

title   = Umbrella pulling simulation
define  = -DPOSRES_A


One thing I will advise (as I keep having to do this privately as people ask 
about my tutorial): do not follow the tutorial too literally.  For general 
protein-ligand complexes, it is *NOT* appropriate to assume one-dimensional 
pulling or applying position restraints to the protein.  Our paper (from which 
the tutorial was derived) describes the somewhat unique case we were dealing 
with.  For a protein-ligand complex, which is spherically symmetrical, treating 
it the same way is inappropriate.


-Justin


; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 100; 1 ns
nstcomm = 50
; Output parameters
nstxout = 5000   ; every 10 ps
nstvout = 5000
nstfout = 5000
nstxtcout   = 5000   ; every 1 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.2
rcoulomb= 1.2
rvdw= 1.2
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein_CHL  Water_and_ions
tau_t   = 0.5   0.5
ref_t   = 310   310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Chain_A
pull_group1 = Chain_B
pull_rate1  = 0.1   ; 0.1 nm per ps
pull_k1 = 836.8 ; kJ mol^-1 nm^-2

but ater 6 steps I got the following error:

Distance of pull group 1 (11.850665 nm) is larger than 0.49 times the box
size 12.092276)

Should I increase all the box dimensions or just z dimension?


Regards,
Farideh


On Sun, Oct 30, 2016 at 7:50 AM, Justin Lemkul  wrote:




On 10/30/16 12:03 AM, faride badalkhani wrote:


Dear all,

I want to define z axis as the reaction coordinate in a series of umbrella
sampling simulations. As a first step, I use the editconf -prince to
orient
the ligand along the x axis and then I change the x and z columns in an



x and z columns of what?  If you have an orientation aligned along x, and
you want it aligned along z, it's a simple use of editconf -rotate 0 90 0

editor. But, every time I get error at pulling step. Could you tell me what

is wrong?



No, because you haven't told us what the exact error is and all the steps
you took in between.  There's a lot of work that goes on between setting up
an orientation and actually running a simulation.

-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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==

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

Department of Pharm

Re: [gmx-users] Questions about free energy calculation tutorial

[Justin Lemkul]

On 11/1/16 9:02 AM, gozde ergin wrote:

This is a generic simulation failure message, indicating that your system is 
blowing up.  This could be due to any number of reasons, but without more 
details it's pointless to guess.


If I do not include the Na ion in decoupling I do not have this warning.
If I do not decouple Na ion still I need to make the charge of this molecule 
zero otherwise system charge becomes +1.


Decoupling the Na+ ion will mean your resulting dG value includes the hydration 
free energy of Na+, which it doesn't sound like you're interested in.


My purpose is doing the same thing with SDS that you did with Methane. And as 
SDS has Na ion I thought I need also to decouple it.
Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
Last question even if I do not decouple the Na ion I need to make it charge 
zero, right?



You can decouple atomic and molecular ions, there are just additional 
considerations like an interface potential to calculate.  See, e.g. work by 
Benoit Roux.


-Justin


Thanks in advance.

On 01 Nov 2016, at 13:21, Justin Lemkul  wrote:



On 11/1/16 7:31 AM, gozde ergin wrote:

Hi Justin,

I would like to ask one question related to this tutorial. I do the same thing 
with using SDS (Sodium dodecyl sulfate) molecule.
As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate part. 
However in order to estimate the free energy of SDS salvation in water I need 
to decouple the all SDS molecule. Since couple-moltype accept only one types of 
molecule, I hacked the topology and put all atoms I want to decouple in the 
same [moleculetype] :

[ moleculetype ]
; name  nrexcl
SDS  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
1 SL  1  SDS  S  1  0.00032.0600   ; qtot  
1.330
2OSL  1  SDSOS1  2  0.00015.9994   ; qtot  
1.050
3O2L  1  SDSOS2  3  0.00015.9994   ; qtot  
0.400
4O2L  1  SDSOS3  4  0.00015.9994   ; qtot 
-0.250
5O2L  1  SDSOS4  5  0.00015.9994   ; qtot 
-0.900
 .
 .
   25   HAL2  1  SDSH71 25  0.000 1.0080   ; qtot 
-1.090
   26   HAL2  1  SDSH72 26  0.000 1.0080   ; qtot 
-1.000
   27   CTL2  1  SDS C8 27  0.00012.0110   ; qtot 
-1.180
.
.
   42   HAL3  1  SDS   H123 42  0.000 1.0080   ; qtot 
-1.000
   43SOD  2  SDSSOD 43  0.00022.9898   ; qtot  
1.000
.

However I get this warning during the simulation :

WARNING: Listed nonbonded interaction between particles 25 and 43
at distance 2.303 which is larger than the table limit 2.200 nm.

Do you have any idea how could I get rid off this warning?



This is a generic simulation failure message, indicating that your system is 
blowing up.  This could be due to any number of reasons, but without more 
details it's pointless to guess.


Also does the hacked .top file seem correct?



Decoupling the Na+ ion will mean your resulting dG value includes the hydration 
free energy of Na+, which it doesn't sound like you're interested in.

-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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--
==

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] Simulation of a solid surface within Gromacs

[Justin Lemkul]

On 11/1/16 8:44 AM, Kamps, M. wrote:

Dear GMX-users,


First of all, I'm sorry if my question is a stupid one. I'm pretty new to
Gromacs and I'm trying to do my best to figure it all out.

I'm trying to work with a solid surface within Gromacs. The final goal of
my simulation is to analyse the behaviour of certain proteins on a metallic
or ceramic substrate and to find the energies related to this system. I'm
having difficulties when trying to implement a surface in Gromacs.


When I create a surface in, for instance, Avogadro or VMD Inorganic
Builder, it is possible to create a .pdb file of such a structure. However,
none of the forcefields can handle the residues, and the error: "Residue
'XXX' not found in residue topology database" arises. The User Manual gives
several options here, but I'm not sure how to approach this problem. In the
manual these options are mentioned:


*If you want a topology
 for an
arbitrary molecule, you cannot use pdb2gmx
 (unless
you build the .rtp
 entry
yourself). You will have to build it by hand, or use another program (such
as x2top  or
one of the scripts contributed by users
) to build the .top
file .*
*- see if there is a different name being used for the residue
 in the residue
database 
and rename as appropriate,*

*- parameterize
 the residue
/ molecule yourself (lots of work, even for an expert),*

*- find a topology file
 for the
molecule, convert it to an .itp file
 and
include it in your .top file
,*

*- use another force field
 which has
parameters available for this,*


*- search the primary literature for publications for parameters for the
residue that are consistent with the force field that is being used*

Based on the first sentence, I cannot use pdb2gmx and therefore have to
build the topology myself. How can I do such a thing? Is there a (simple)
guide available?

Also, am I taking the right steps for creating a surface within Gromacs? Is
there a (easier) different way?



x2top is the only GROMACS tool that will be of any use here.  You will have to 
write a suitable .n2t file (see the manual) for whatever species you're dealing 
with.


-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] help me

[Rob Jehan]

 In simulation  using  following command 
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr 
 i need to convert dppc128.pdb to dppc128.gro using this command 

pdb2gmx -f dppc128.pdb -o dppc128.gro -ignh -ter -water spc but
now i am getting this fatal error.
Fatal error:There were46 missing atoms in molecule Other, if you want to use 
thisincomplete topology anyhow, use the option -missing
please sort it out
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Re: [gmx-users] qmmm

[Groenhof, Gerrit]

Looks more like an issue running orca than with gromacs and it seems that 
you're trying to run orca with mpi, but don't have an mpirun in your path. Can 
you run ORCA stand-alone with the input file generated with gromacs? If it is 
orca related, please contact Orca crew.

Best,

Gerrit



Message: 4
Date: Tue, 1 Nov 2016 23:38:04 +
From: "Adamu, Aliyu" 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] qmmm
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Dear Gerrit,

thanks a lot for your email. when i used "export BASENAME=topol" as you 
suggested, that particular error was solved. but yet i got another error 
reading as:

starting mdrun 'Protein'
5000 steps,  5.0 ps.
Calling '/home/birg/orca//orca topol.inp >> topol.out'
sh: 1: mpirun: not found
ORCA finished by error termination in ORCA_GTOInt
Segmentation fault (core dumped)

I dont know what is wrong, because i am running the calculation on just one PC

many thanks
Aliyu Adamu

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Groenhof, 
Gerrit [ggro...@gwdg.de]
Sent: Tuesday, November 1, 2016 12:45 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] qmmm

depending on the shell try using "export BASENAME=topol" or "setenv BASENAME 
topop' instead. You can check if things worked by typing echo $BASENAME which 
should be topol.

I am surprised you did not get an error message form the shell after typing 
these lines...

Gerrit

Message: 3
Date: Tue, 1 Nov 2016 10:57:07 +
From: "Adamu, Aliyu" 
To: "gmx-us...@gromacs.org" 
Subject: [gmx-users] qmmm
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Hello Justin

could you please help me out on how to get over this problem? I want to run 
QM/MM calculation in GROMACS 4.6.7 and ORCA version 3.03. before i run the 
mdrun command i set the environment variables: BASENAME and ORCA_PATH by typing 
the following command in the shell:

BASENAME=topol
ORCA_PATH=/home/birg/orca

But when i type the command for the mdrun as:

mdrun -v -c qmmm1out.gro

it gives me error massage that reads as:

---
Program mdrun, VERSION 4.6.7
Source code file: /home/birg/Downloads/gromacs-4.6.7/src/mdlib/qm_orca.c, line: 
86

Fatal error:
$BASENAME not set

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I dont know why is indicating basename not set. please help me out?

many thanks
Aliyu Adamu

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