[gmx-users] Bond energy difference between CHARMM and GROMACS

[Yvon Wong]

I try to compare the energy in CHARMM and GROMACS.
After running 4 systems I found the dihedral energies are the same, but the
bond energies are different.
Can somebody help me to solve this problem?

(1)Only one residue: MET

Bond:

0.44*4.18   =   1.839 (CHARMM)  >  2.587 (GROMACS)   (different)
Dihedral:

3.687* 4.18 = 15.4116 (CHRAMM)  > 15.4448 (GROMACS)  (the same)

(2)Only one residue: GLY
BONDS:

  0.34243*4.18=  1.431  ===> 1.209


Dihedrals
1.77911*4.18 = 7.436  ===> 7.447

(3)5 -residue:  ASN GLY PHE TRP THR
BONS:

4.82777* 4.18=20.1800   >   22.58


DIHE:
37.82747*4.18 =  158.1188   >  158.504

(4)20- residue:  GLY LYS MET PHE SER TRP TYR VAL ALA ARG CYS VAL PRO
TRP MET SER SER LYS LYS MET
BONDS

17.48049 * 4.18 =73.068  ===>   78.64


DIHE

185.71* 4.18  =   776.26  ===>  777.32
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[gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

[spss4]

--- Begin Message ---

Hello,
I am a new user of gromacs. I am trying to calculate SASA for a protein
system. I have used the command

 gmx sasa -f traj.trr -s md.tpr -o sasa.xvg -n index.ndx

 From this I can only get the total SASA but I want hydrophobic and
hydrophilic SASA separately. I know it can be done using g_sas command for
older version. But I am using newer version of gromacs (gromacs-2016.1).
Please help me to solve this problem. Thanks in advance.

Sunipa Sarkar
--- End Message ---
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Re: [gmx-users] topology

[RAHUL SURESH]

So it is mandatory to add

> *; Include ligand topology
> #include "drug.itp"*

In top file.?


On Tue, 28 Mar 2017 at 2:08 AM, Justin Lemkul  wrote:

>
>
> On 3/27/17 3:23 PM, RAHUL SURESH wrote:
> > What if I run my protein-ligand simulation with out using
> >
>
> >
> > in the topology file generated using pdb2gmx.
> >
> > but i have added my ligand in protein.gro file.
> >
>
> Then you'll get a fatal error from grompp about mismatching number of
> atoms or
> atom names.
>
> -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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] protein-ligand

[RAHUL SURESH]

How will I add ligand .gro file in protein .gro file to make a complex .?
On Tue, 28 Mar 2017 at 2:12 AM, Justin Lemkul  wrote:

>
>
> On 3/27/17 4:02 PM, RAHUL SURESH wrote:
> > In protein-ligand simulation using charmm36ff, how to generate gro file
> for
> > ligand to add it to the protein gro file?
> >
>
> You don't strictly need a .gro file, since GROMACS can handle PDB and other
> formats, but in short, you can convert between formats easily with
> editconf.
>
> -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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

Sorry it was a typing mistake..it is actually

1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx

> del 2
Removed group 2 'SOL'
 > del 1
Removed group 1 'Water'
 > del 0
Removed group 0 'System'
> a H1 H2 H3 OW
Found xxx atoms with name H1 H2 H3 OW
0 H1 H2 H3 OW : xxx atoms
> q

2]Then, Using the index to calculate the pair correlation function for all
frames:-
gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg

Available static index groups:
 Group  0 "H1_H2_H3 OW" (xxx atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line,  for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

3] View the plot:

xmgrace rdf_Hn-OW.xvg

and if i view the obtained graphs in xmgrace i am getting only two kinds of
graphs...ie.,
(a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
(b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..

My doubts are..
1)What is this only two kinds of graphs am i getting..?? ,
2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx.,
2] gmx rdf . 3] xmgrace. are correct in accordance..
3)Or is there any mistake that i am doing..?? Can anybody rectify my
mistakes if any..??

as you have told how to put  Hn atoms in one group and the Ow in
another...??




   Sent with Mailtrack


On Tue, Mar 28, 2017 at 2:10 AM, Justin Lemkul  wrote:

>
>
> On 3/27/17 3:55 PM, Dilip H N wrote:
>
>> i want to calculate RDF of glycine  of Hn-OW, Hn-HW, Ha-OW, Ha-HW,  Ca-OW,
>>  etc.,
>> So my commands were as follows...
>>
>> 1] To make indexes:-
>> gmx make_ndx -f md.gro -o Hn-OW.ndx
>>
>> del 2
>>>
>> Removed group 2 'SOL'
>>  > del 1
>> Removed group 1 'Water'
>>  > del 0
>> Removed group 0 'System'
>>
>>> a H1 H2 H3 OW
>>>
>> Found xxx atoms with name H1 H2 H3 OW
>> 0 HA1_HA2_OW : xxx atoms
>>
>>> q
>>>
>>
>>
>> 2]Then, Using the index to calculate the pair correlation function for all
>> frames:-
>> gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg
>>
>> Available static index groups:
>>  Group  0 "HA1_HA2_OW" (xxx atoms)
>> Specify a selection for option 'ref'
>> (Reference selection for RDF computation):
>> (one per line,  for status/groups, 'help' for help)
>>
>>> 0
>>>
>> Selection '0' parsed
>>
>>> cntrl+d
>>>
>> Last frame   1000 time 1.000
>> Analyzed 1001 frames, last time 1.000
>>
>> 3] View the plot:
>>
>> xmgrace rdf_Hn-OW.xvg
>>
>> and if i view the obtained graphs in xmgrace i am getting only two kinds
>> of
>> graphs...ie.,
>> (a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
>> (b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..
>>
>> My doubts are..
>> 1)What is this only two kinds of graphs am i getting..?? ,
>> 2)I hope the above procedure to get RDF ie., commands 1] gmx
>> make_ndx.,
>> 2] gmx rdf . 3] xmgrace. are correct in accordance..
>> 3)Or is there any mistake that i am doing..?? Can anybody rectify my
>> mistakes if any..??
>>
>>
> You're probably just getting a bunch of garbage.  You're apparently
> merging the alpha hydrogen atoms and water oxygens into one group, which
> makes no sense at all.  If you want Ha-Ow RDF, then the Ha* atoms should be
> in one group and the Ow in another.
>
> -Justin
>
>
>>
>>
>>
>>    Sent with Mailtrack
>> > ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>>
>> On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 3/27/17 8:50 AM, Dilip H N wrote:
>>>
>>> Thanks Justin,

 But my doubts are..
 1] after energy minimization of both glycine non zwitterionic form and
 zwitterionic form with water, if i visualize it in vmd, the bond between
 some of the water molecules are broken.. why is this so..??


>>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>>> Boundary_Conditions
>>>
>>> What you see on the VMD display is its best guess as to how things are
>>> connected.  That's not always right.  The topology is always right.
>>> That's
>>> why trjconv exists.
>>>
>>> 2] and ran nvt,npt,md simulations respectively...and during analysis
>>> part i
>>>
 am getting only similar two types of RDF graphs...why is this
 happening...i
 have made all the indexing, etc., proper...


 You have provided no useful information about what these RDF plots are
>>> or
>>> how you acquired them, so there's no point for either of us in guessing.
>>> Maybe the distribution(s) that you're looking at simply don't vary as a
>>> function of protonation state.
>>>
>>> Is there any tutorials for these as an example..?? solving this would
>>> help
>>>
 me a lot


 It's an amino acid in water; it's as easy of a protein s

Re: [gmx-users] Help in a thermalization

[Justin Lemkul]

On 3/27/17 5:17 PM, Graziele Bortolini wrote:

The error 3 was solved, but when I change to cutoff-scheme = group, I
receive:

"Fatal error:
The largest charge group contains 66 atoms. The maximum is 32."

I've tried to make this before, and I saw your answer about this error in
this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/061989.html
But I don't understand what I need to do.



Apparently your whole molecule is assigned to a single charge group, which is 
not supported.  In this specific case (infinite cutoffs), charge groups are 
irrelevant, but in general the idea is that chemical moieties are assigned to 
groups of integral charge (e.g. -CH3, -NH2, -CH2OH, etc).  See the parent force 
field for examples.  Some (most) force fields do not use charge groups at all, 
so you can just assign every atom to its own charge group and not worry about it 
(again, because your nonbonded setup doesn't depend on it).


-Justin



2017-03-27 17:56 GMT-03:00 Justin Lemkul :




On 3/27/17 4:50 PM, Graziele Bortolini wrote:


I do it too, my .mdp file now is like :
-
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 50
nstcomm = 1
comm-mode = angular
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0
vdwtype = shift
rvdw = 0
tcoupl = berendsen
tc_grps = system
ref_t = 300.0
tau_t = 0.1
pcoupl = berendsen
ref_p = 1.000
compressibility = 4.5e-5
tau_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 300.0
pbc = no
--
but I receive another errors messages:


ERROR 1 [file teste2.mdp]:
  With Verlet lists only full pbc or pbc=xy with walls is supported

ERROR 2 [file teste2.mdp]:
  The box volume is required for calculating rlist from the energy drift
  with verlet-buffer-tolerance > 0. You are using at least one unbounded
  dimension, so no volume can be computed. Either use a finite box, or set
  rlist yourself together with verlet-buffer-tolerance = -1.



Both of these are solved with cutoff-scheme = group.

ERROR 3 [file teste2.mdp]:

  With switched vdw forces or potentials, rvdw-switch must be < rvdw



You have an infinite cutoff, there's nothing to switch or shift.  You need
vdwtype = cutoff.


-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] Help in a thermalization

[Graziele Bortolini]

The error 3 was solved, but when I change to cutoff-scheme = group, I
receive:

"Fatal error:
The largest charge group contains 66 atoms. The maximum is 32."

I've tried to make this before, and I saw your answer about this error in
this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/061989.html
But I don't understand what I need to do.


2017-03-27 17:56 GMT-03:00 Justin Lemkul :

>
>
> On 3/27/17 4:50 PM, Graziele Bortolini wrote:
>
>> I do it too, my .mdp file now is like :
>> -
>> cpp = /lib/cpp
>> integrator = md
>> dt = 0.001
>> nsteps = 50
>> nstcomm = 1
>> comm-mode = angular
>> nstxout = 0
>> nstvout = 0
>> nstlog = 0
>> nstenergy = 50
>> nstxtcout = 50
>> energygrps = PSB
>> nstlist = 10
>> ns_type = grid
>> rlist = 0
>> coulombtype = Cut-off
>> optimize_fft = yes
>> rcoulomb = 0
>> vdwtype = shift
>> rvdw = 0
>> tcoupl = berendsen
>> tc_grps = system
>> ref_t = 300.0
>> tau_t = 0.1
>> pcoupl = berendsen
>> ref_p = 1.000
>> compressibility = 4.5e-5
>> tau_p = 1.0
>> pcoupltype = isotropic
>> gen_vel = yes
>> gen_temp = 300.0
>> pbc = no
>> --
>> but I receive another errors messages:
>>
>>
>> ERROR 1 [file teste2.mdp]:
>>   With Verlet lists only full pbc or pbc=xy with walls is supported
>>
>> ERROR 2 [file teste2.mdp]:
>>   The box volume is required for calculating rlist from the energy drift
>>   with verlet-buffer-tolerance > 0. You are using at least one unbounded
>>   dimension, so no volume can be computed. Either use a finite box, or set
>>   rlist yourself together with verlet-buffer-tolerance = -1.
>>
>>
> Both of these are solved with cutoff-scheme = group.
>
> ERROR 3 [file teste2.mdp]:
>>   With switched vdw forces or potentials, rvdw-switch must be < rvdw
>>
>>
> You have an infinite cutoff, there's nothing to switch or shift.  You need
> vdwtype = cutoff.
>
>
> -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
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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>



-- 
Att.
G. Bortolini
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Re: [gmx-users] Help in a thermalization

[Justin Lemkul]

On 3/27/17 4:50 PM, Graziele Bortolini wrote:

I do it too, my .mdp file now is like :
-
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 50
nstcomm = 1
comm-mode = angular
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0
vdwtype = shift
rvdw = 0
tcoupl = berendsen
tc_grps = system
ref_t = 300.0
tau_t = 0.1
pcoupl = berendsen
ref_p = 1.000
compressibility = 4.5e-5
tau_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 300.0
pbc = no
--
but I receive another errors messages:


ERROR 1 [file teste2.mdp]:
  With Verlet lists only full pbc or pbc=xy with walls is supported

ERROR 2 [file teste2.mdp]:
  The box volume is required for calculating rlist from the energy drift
  with verlet-buffer-tolerance > 0. You are using at least one unbounded
  dimension, so no volume can be computed. Either use a finite box, or set
  rlist yourself together with verlet-buffer-tolerance = -1.



Both of these are solved with cutoff-scheme = group.


ERROR 3 [file teste2.mdp]:
  With switched vdw forces or potentials, rvdw-switch must be < rvdw



You have an infinite cutoff, there's nothing to switch or shift.  You need 
vdwtype = cutoff.


-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] Help in a thermalization

[Graziele Bortolini]

I do it too, my .mdp file now is like :
-
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 50
nstcomm = 1
comm-mode = angular
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0
vdwtype = shift
rvdw = 0
tcoupl = berendsen
tc_grps = system
ref_t = 300.0
tau_t = 0.1
pcoupl = berendsen
ref_p = 1.000
compressibility = 4.5e-5
tau_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 300.0
pbc = no
--
but I receive another errors messages:


ERROR 1 [file teste2.mdp]:
  With Verlet lists only full pbc or pbc=xy with walls is supported

ERROR 2 [file teste2.mdp]:
  The box volume is required for calculating rlist from the energy drift
  with verlet-buffer-tolerance > 0. You are using at least one unbounded
  dimension, so no volume can be computed. Either use a finite box, or set
  rlist yourself together with verlet-buffer-tolerance = -1.

ERROR 3 [file teste2.mdp]:
  With switched vdw forces or potentials, rvdw-switch must be < rvdw
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Re: [gmx-users] Help in a thermalization

[Justin Lemkul]

On 3/27/17 4:12 PM, Graziele Bortolini wrote:

When I tried to do a thermalization for a PSB molecule (it has 66 atoms),
in vacuum, the molecule rotate around the center of mass. This's my .mdp
file:
---
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 50
nstcomm = 1
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0.4
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0.8
vdwtype = shift
rvdw = 0.8
tcoupl = berendsen
tc_grps = system
ref_t = 300.0
tau_t = 0.1
pcoupl = berendsen
ref_p = 1.000
compressibility = 4.5e-5
tau_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 300.0
pbc = xyz
---
So, I tried to put the "comm-mode = angular", it supposedly remove center
of mass translation and rotation. But when I do it I receive the following
message:

"WARNING 1 :
  Removing the rotation around the center of mass in a periodic system,
  this can lead to artifacts. Only use this on a single (cluster of)
  molecules. This cluster should not cross periodic boundaries."

What I'm doing wrong?



You're not running in vacuo.  By using finite cutoffs and using PBC, you're 
simulating a molecule in some sparsely populated pseudocrystalline state.  To 
run in vacuo, set all cutoffs to zero (which means infinite), use no PBC, and 
set comm-mode = angular.


-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] protein-ligand

[Justin Lemkul]

On 3/27/17 4:02 PM, RAHUL SURESH wrote:

In protein-ligand simulation using charmm36ff, how to generate gro file for
ligand to add it to the protein gro file?



You don't strictly need a .gro file, since GROMACS can handle PDB and other 
formats, but in short, you can convert between formats easily with editconf.


-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 Glycine structure

[Justin Lemkul]

On 3/27/17 3:55 PM, Dilip H N wrote:

i want to calculate RDF of glycine  of Hn-OW, Hn-HW, Ha-OW, Ha-HW,  Ca-OW,
 etc.,
So my commands were as follows...

1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx


del 2

Removed group 2 'SOL'
 > del 1
Removed group 1 'Water'
 > del 0
Removed group 0 'System'

a H1 H2 H3 OW

Found xxx atoms with name H1 H2 H3 OW
0 HA1_HA2_OW : xxx atoms

q



2]Then, Using the index to calculate the pair correlation function for all
frames:-
gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg

Available static index groups:
 Group  0 "HA1_HA2_OW" (xxx atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line,  for status/groups, 'help' for help)

0

Selection '0' parsed

cntrl+d

Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

3] View the plot:

xmgrace rdf_Hn-OW.xvg

and if i view the obtained graphs in xmgrace i am getting only two kinds of
graphs...ie.,
(a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
(b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..

My doubts are..
1)What is this only two kinds of graphs am i getting..?? ,
2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx.,
2] gmx rdf . 3] xmgrace. are correct in accordance..
3)Or is there any mistake that i am doing..?? Can anybody rectify my
mistakes if any..??



You're probably just getting a bunch of garbage.  You're apparently merging the 
alpha hydrogen atoms and water oxygens into one group, which makes no sense at 
all.  If you want Ha-Ow RDF, then the Ha* atoms should be in one group and the 
Ow in another.


-Justin






   Sent with Mailtrack


On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  wrote:




On 3/27/17 8:50 AM, Dilip H N wrote:


Thanks Justin,

But my doubts are..
1] after energy minimization of both glycine non zwitterionic form and
zwitterionic form with water, if i visualize it in vmd, the bond between
some of the water molecules are broken.. why is this so..??



http://www.gromacs.org/Documentation/Terminology/Periodic_
Boundary_Conditions

What you see on the VMD display is its best guess as to how things are
connected.  That's not always right.  The topology is always right.  That's
why trjconv exists.

2] and ran nvt,npt,md simulations respectively...and during analysis part i

am getting only similar two types of RDF graphs...why is this
happening...i
have made all the indexing, etc., proper...



You have provided no useful information about what these RDF plots are or
how you acquired them, so there's no point for either of us in guessing.
Maybe the distribution(s) that you're looking at simply don't vary as a
function of protonation state.

Is there any tutorials for these as an example..?? solving this would help

me a lot



It's an amino acid in water; it's as easy of a protein system as there is.
There's nothing special about it that requires a tutorial.

-Justin



   Sent with Mailtrack



On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  wrote:




On 3/23/17 2:05 PM, Dilip H N wrote:

Hello,


I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and
in
the first step if i do the energy minimization and then visualizes the
mixture, the glycine is no more in its pure form as before instead it
has
been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
bonds with water are also broken. How can i solve these both issues..??


Glycine didn't convert between forms.  That's impossible; bonds can't

break or form in a molecular mechanical process.  The termini are exactly
what you assigned them to be.  If you want them to be something else, you
have to assign them as such with pdb2gmx.  Though you should note that
NH2
and COOH can't coincide at any real pH value.

-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 P

Re: [gmx-users] Is My NPT Density High?

[Justin Lemkul]

On 3/27/17 3:28 PM, Jonathan Saboury wrote:

Hello all,

I have a system with a protein, lipid bilayer, and water/ions. I am getting
a density of
1034 kg/m^3. I would have expected it to be lower because of the lipids. Is
this a reasonable density for such a system?



An overall density of such a heterogeneous system is not useful or meaningful. 
Get a density profile as a function of z using gmx density.  The headgroup 
region can be especially tightly packed.


-Justin


Image of system: http://oi64.tinypic.com/35jaykl.jpg
NPT_density.xvg: https://pastebin.com/raw/UPZiRf1t

If you need any other info please let me know, thank you!

- Jonathan



--
==

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] topology

[Justin Lemkul]

On 3/27/17 3:23 PM, RAHUL SURESH wrote:

What if I run my protein-ligand simulation with out using

*; Include ligand topology
#include "drug.itp"*

in the topology file generated using pdb2gmx.

but i have added my ligand in protein.gro file.



Then you'll get a fatal error from grompp about mismatching number of atoms or 
atom names.


-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 in a thermalization

[Graziele Bortolini]

When I tried to do a thermalization for a PSB molecule (it has 66 atoms),
in vacuum, the molecule rotate around the center of mass. This's my .mdp
file:
---
cpp = /lib/cpp
integrator = md
dt = 0.001
nsteps = 50
nstcomm = 1
nstxout = 0
nstvout = 0
nstlog = 0
nstenergy = 50
nstxtcout = 50
energygrps = PSB
nstlist = 10
ns_type = grid
rlist = 0.4
coulombtype = Cut-off
optimize_fft = yes
rcoulomb = 0.8
vdwtype = shift
rvdw = 0.8
tcoupl = berendsen
tc_grps = system
ref_t = 300.0
tau_t = 0.1
pcoupl = berendsen
ref_p = 1.000
compressibility = 4.5e-5
tau_p = 1.0
pcoupltype = isotropic
gen_vel = yes
gen_temp = 300.0
pbc = xyz
---
So, I tried to put the "comm-mode = angular", it supposedly remove center
of mass translation and rotation. But when I do it I receive the following
message:

"WARNING 1 :
  Removing the rotation around the center of mass in a periodic system,
  this can lead to artifacts. Only use this on a single (cluster of)
  molecules. This cluster should not cross periodic boundaries."

What I'm doing wrong?
-- 
Att.
G. Bortolini
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[gmx-users] protein-ligand

[RAHUL SURESH]

In protein-ligand simulation using charmm36ff, how to generate gro file for
ligand to add it to the protein gro file?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

i want to calculate RDF of glycine  of Hn-OW, Hn-HW, Ha-OW, Ha-HW,  Ca-OW,
 etc.,
So my commands were as follows...

1] To make indexes:-
gmx make_ndx -f md.gro -o Hn-OW.ndx

> del 2
Removed group 2 'SOL'
 > del 1
Removed group 1 'Water'
 > del 0
Removed group 0 'System'
> a H1 H2 H3 OW
Found xxx atoms with name H1 H2 H3 OW
0 HA1_HA2_OW : xxx atoms
> q


2]Then, Using the index to calculate the pair correlation function for all
frames:-
gmx rdf -f md.trr -s md.tpr -n Hn-OW.ndx -o rdf_Hn-OW.xvg

Available static index groups:
 Group  0 "HA1_HA2_OW" (xxx atoms)
Specify a selection for option 'ref'
(Reference selection for RDF computation):
(one per line,  for status/groups, 'help' for help)
> 0
Selection '0' parsed
>cntrl+d
Last frame   1000 time 1.000
Analyzed 1001 frames, last time 1.000

3] View the plot:

xmgrace rdf_Hn-OW.xvg

and if i view the obtained graphs in xmgrace i am getting only two kinds of
graphs...ie.,
(a) for Hn-OW,Ha-OW etc, graphs are same for OW end indexing and
(b) for Hn-HW,Ha-HW etc., graphs are same for HW end indexing..

My doubts are..
1)What is this only two kinds of graphs am i getting..?? ,
2)I hope the above procedure to get RDF ie., commands 1] gmx make_ndx.,
2] gmx rdf . 3] xmgrace. are correct in accordance..
3)Or is there any mistake that i am doing..?? Can anybody rectify my
mistakes if any..??





   Sent with Mailtrack


On Mon, Mar 27, 2017 at 10:27 PM, Justin Lemkul  wrote:

>
>
> On 3/27/17 8:50 AM, Dilip H N wrote:
>
>> Thanks Justin,
>>
>> But my doubts are..
>> 1] after energy minimization of both glycine non zwitterionic form and
>> zwitterionic form with water, if i visualize it in vmd, the bond between
>> some of the water molecules are broken.. why is this so..??
>>
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
> Boundary_Conditions
>
> What you see on the VMD display is its best guess as to how things are
> connected.  That's not always right.  The topology is always right.  That's
> why trjconv exists.
>
> 2] and ran nvt,npt,md simulations respectively...and during analysis part i
>> am getting only similar two types of RDF graphs...why is this
>> happening...i
>> have made all the indexing, etc., proper...
>>
>>
> You have provided no useful information about what these RDF plots are or
> how you acquired them, so there's no point for either of us in guessing.
> Maybe the distribution(s) that you're looking at simply don't vary as a
> function of protonation state.
>
> Is there any tutorials for these as an example..?? solving this would help
>> me a lot
>>
>>
> It's an amino acid in water; it's as easy of a protein system as there is.
> There's nothing special about it that requires a tutorial.
>
> -Justin
>
>
>>    Sent with Mailtrack
>> > ral=cy16f01.di...@nitk.edu.in&idSignature=22>
>>
>>
>> On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 3/23/17 2:05 PM, Dilip H N wrote:
>>>
>>> Hello,

 I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and
 in
 the first step if i do the energy minimization and then visualizes the
 mixture, the glycine is no more in its pure form as before instead it
 has
 been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
 bonds with water are also broken. How can i solve these both issues..??


 Glycine didn't convert between forms.  That's impossible; bonds can't
>>> break or form in a molecular mechanical process.  The termini are exactly
>>> what you assigned them to be.  If you want them to be something else, you
>>> have to assign them as such with pdb2gmx.  Though you should note that
>>> NH2
>>> and COOH can't coincide at any real pH value.
>>>
>>> -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
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postd

Re: [gmx-users] Extracting Energy of Individual Molecules From Energy File

[Kelechi Okoroafor]

Thank you very much, Justin!


-- 
Best wishes,
Kelechi
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[gmx-users] Is My NPT Density High?

[Jonathan Saboury]

Hello all,

I have a system with a protein, lipid bilayer, and water/ions. I am getting
a density of
1034 kg/m^3. I would have expected it to be lower because of the lipids. Is
this a reasonable density for such a system?

Image of system: http://oi64.tinypic.com/35jaykl.jpg
NPT_density.xvg: https://pastebin.com/raw/UPZiRf1t

If you need any other info please let me know, thank you!

- Jonathan
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[gmx-users] topology

[RAHUL SURESH]

What if I run my protein-ligand simulation with out using

*; Include ligand topology
#include "drug.itp"*

in the topology file generated using pdb2gmx.

but i have added my ligand in protein.gro file.



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] solvate with hexagonal box

[Mark Abraham]

Hi,

Sounds like there is something worth improving, although I can't answer
your questions right now. Please open an issue on
https://redmine.gromacs.org and attach a tarball of suitable inputs for the
two(?) cases.

Mark

On Mon, 27 Mar 2017 13:54 Erik Marklund  wrote:

> Dear gmx-users,
>
> We are trying to merge a box containing a peripheral membrane protein with
> another box generated with memgen. Both boxes are hexagonal and exactly the
> same size,Naively, we thought that gmx solvate -cp protein.gro -cs
> membrane_and_water.gro would do the trick. Unfortunately, this causes gmx
> solvate to crash:
>
> Generating solvent configuration
> Will generate new solvent configuration of 1x2x1 boxes
> Solvent box contains 99373 atoms in 28208 residues
> Removed 12253 solvent atoms due to solvent-solvent overlap
> Removed 5122 solvent atoms due to solute-solvent overlap
> Sorting configuration
> Found 2 different molecule types:
>POPE (  52 atoms):   233 residues
> SOL (   3 atoms): 23294 residues
> gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0:
> pointer being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap: 6
>
> So we then tried to remove the membrane, keeping only the water, and use
> that system as the argument for -cs. Gmx solvate doesn’t crash now, but the
> output file has strange gaps of some size in the water parts, which cannot
> be explained by the removed lipids. Can gmx solvate not handle
> non-orthogonal boxes as arguments for -cs?
>
> The whole point in doing it this way was to avoid water molecules being
> inserted in the membrane. Perhaps overkill, but I am quite surprised at how
> bad things went with gmx solvate.
>
> Kind regards,
> Erik
>
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> --
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Re: [gmx-users] Unbiased or biased

[Justin Lemkul]

On 3/27/17 11:02 AM, m g wrote:

Dear Justin Lemkul,I red your tutorial "Umbrella Sampling", I want to know
about unbiased and biased method. you sad that used biasing potential. which
parameter in md files refers to biased? how can i used unbiased method? what


An applied external potential is a bias, i.e. the harmonic restraint being 
applied by the pull code.



is difference between unbiased and biased exactly? I used this method that
you learned in this tutorial for pulling a drug molecule across the POPC
membrane, but I don't know in my work this PMF is unbiased or biased. would
you pleas help me?Thanks



The simulations that generate the distance distributions are biased because 
there is an external potential applied to them.  The PMF, by definition, is 
unbiased (this the point of WHAM, and if you haven't read the Kumar paper and 
those cited within, stop what you're doing and read those now).


-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] Extracting Energy of Individual Molecules From Energy File

[Justin Lemkul]

On 3/27/17 9:20 AM, Kelechi Okoroafor wrote:

Hello, All.

Please is it possible to extract the different components of energy (i.e.
Bond, Angle, Coulombic and LJ) for individual molecule from the *.edr file?



Not from the .edr file, but if you extract the coordinates of that molecule from 
the trajectory, create a matching .tpr, and use mdrun -rerun to compute the 
energies.


-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

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Re: [gmx-users] Regarding Glycine structure

[Justin Lemkul]

On 3/27/17 8:50 AM, Dilip H N wrote:

Thanks Justin,

But my doubts are..
1] after energy minimization of both glycine non zwitterionic form and
zwitterionic form with water, if i visualize it in vmd, the bond between
some of the water molecules are broken.. why is this so..??


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

What you see on the VMD display is its best guess as to how things are 
connected.  That's not always right.  The topology is always right.  That's why 
trjconv exists.



2] and ran nvt,npt,md simulations respectively...and during analysis part i
am getting only similar two types of RDF graphs...why is this happening...i
have made all the indexing, etc., proper...



You have provided no useful information about what these RDF plots are or how 
you acquired them, so there's no point for either of us in guessing.  Maybe the 
distribution(s) that you're looking at simply don't vary as a function of 
protonation state.



Is there any tutorials for these as an example..?? solving this would help
me a lot



It's an amino acid in water; it's as easy of a protein system as there is. 
There's nothing special about it that requires a tutorial.


-Justin



   Sent with Mailtrack


On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  wrote:




On 3/23/17 2:05 PM, Dilip H N wrote:


Hello,

I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in
the first step if i do the energy minimization and then visualizes the
mixture, the glycine is no more in its pure form as before instead it has
been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
bonds with water are also broken. How can i solve these both issues..??



Glycine didn't convert between forms.  That's impossible; bonds can't
break or form in a molecular mechanical process.  The termini are exactly
what you assigned them to be.  If you want them to be something else, you
have to assign them as such with pdb2gmx.  Though you should note that NH2
and COOH can't coincide at any real pH value.

-Justin

--
==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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University of Maryland, Baltimore
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Re: [gmx-users] Secondary structure analysis

[Justin Lemkul]

On 3/27/17 6:48 AM, RAHUL SURESH wrote:

i found a lot libraries missing in dssp.

can i obtain them using
*rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ 
/home/oem/Downloads/dssp*



The dssp binary is all you should need.  It's pre-compiled (though you can get 
the source) for various architectures.


-Justin


On Sun, Mar 26, 2017 at 9:44 PM, Souparno Adhikary 
wrote:


I think dssp is a useful tool for this purpose...

Souparno

On 26 Mar 2017 19:50, "Justin Lemkul"  wrote:




On 3/26/17 8:21 AM, RAHUL SURESH wrote:


I use gromacs 2016.1 version. How to do secondary structure analysis ?



http://manual.gromacs.org/documentation/2016.1/user-guide/
cmdline.html#protein-specific-analysis

-Justin

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School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] forcefield installation on GROMACS 5.1.4

[Justin Lemkul]

On 3/27/17 7:44 AM, Simon Kit Sang Chu wrote:

Hi everyone,

Recently I am looking into PACE
 for my system and
installation of forcefield is required. The files located inside the
forcefield directory is given by -

aminoacids.rtp  cgWater.itp  ffPACE_1.3-c.tdb  ffPACE_1.3.hdb
 ffPACE_1.3-n.tdb
cg216water.gro  ffPACE_1.3.atp  ffPACE_1.3.ddbffPACE_1.3.itp
 ffPACE_1.3.rtp

Compared to the standard forcefields, such as CHARMM and AMBER, there is no
.doc. I located these files in
/usr/local/gromacs/share/gromacs/top/PACE_1.3.ff.

When I tried to implement the forcefield with pdb2gmx, I see no sign of
PACE and option -ff returns error too.

I am new to GROMACS. Would anyone suggest any solution or references that I
should look into?



You need a forcefield.doc file that has the force field name so that pdb2gmx can 
find it.


-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

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Re: [gmx-users] Restraining Protein-ligand distance

[Justin Lemkul]

On 3/27/17 8:42 AM, Juan José Galano Frutos wrote:

Hi there,

I am trying AFEC simulations in complex (ligand-protein), but sometimes I
get the ligands out the binding site, but I dont want that scenary. I was
thinking the situation of applying distance retraints between a ligand and
a protein was already solved in GROMACS version later 5.0... without any
necessity of making a hybrid system. But, I'm using version 5.1, and it
seems that's not possible doing so, because I'm obtaining errors.
Is there currently any happy solution to restraint ligand-protein distance?
or Has one to still go through the unbrella pulling option to do that?



You need distance as well as orientational restraints.  This is done with 
[intermolecular_interactions], which was a new feature in 5.1.  For theory, see 
dx.doi.org/10.1021/ci300505n


-Justin


In the case I need to do a hybrid system what would be a good procedure?

Thank you very much.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)



--
==

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

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Re: [gmx-users] Protein preparation

[Justin Lemkul]

On 3/27/17 2:16 AM, Rasika Kelum wrote:

Thank you Justin. Highly appreciate your help.

If there are missing residues, any suggestions on fixing the protein?



There are plenty of tools to do that; Modeller is one of them.


1. How to find correct sequence? (is there any website to find correct
sequence?)


This should be your first stop in starting your research.  If you don't know the 
sequence or other very fundamental information, stop what you're doing at the 
terminal and pull out the biology literature.



2. How to FIX the sequence (using what software?)


See above.


3. Once residues are fixed how would that affect the geometry of the
protein? Do we have to fix the geometry of protein as well?



Depends on the quality of the reconstruction of missing atoms.  Most programs 
are pretty robust, but a very short energy minimization usually relaxes away any 
problems.


-Justin

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Department of Pharmaceutical Sciences
School of Pharmacy
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20 Penn St.
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Re: [gmx-users] calculation of self energy of protein

[Justin Lemkul]

On 3/27/17 2:02 AM, Saumyak Mukherjee wrote:

Dear Justin,

Is there any way to get just the interaction energy between protein and
water? In this case, the energy should not contain the self or inherent
energy.



Set the protein and water as separate energygrps and extract the relevant 
nonbonded terms with gmx energy.


-Justin


Thanks & regards,
Saumyak

On 27 March 2017 at 11:27, Saumyak Mukherjee 
wrote:


Thank you very much.

On 27 March 2017 at 02:22, Justin Lemkul  wrote:




On 3/26/17 4:49 PM, Saumyak Mukherjee wrote:


Dear Justin,

Thanks for the reply.

I have tried that already. I stripped out the protein trajectory using
trjconv, created an appropriate .tpr file using tpbconv (I am using
GROMACS
4.5.6), and recalculated energy using mdrun -rerun.

But does the resulting .edr file include only the inherent energy of the
protein or does it have information of the interaction energies with the
solvent as well? That precisely is the point I am confused about.

I tried this with a protein in water system and also simulated a dry
protein separately to compare. The energies were way to different from
each
other. Does it mean that the solvent-protein interaction energies are
also
involved?



If you have a protein-only trajectory and a protein-only .tpr file,
there's no possible way for there to be any sort of protein-solvent
interaction energy. The energies of a "wet" and "dry" protein system should
be extremely different.

-Justin


--
==

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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

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--

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in









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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

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Re: [gmx-users] Using the md integrator for calculating free energy of solvation

[Justin Lemkul]

On 3/26/17 9:40 PM, Dan Gil wrote:

Hi,

I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on
calculating free energy of solvation. Is it possible and theoretically
sound to use the md integrator instead of the sd integrator for these
calculations?



Langevin dynamics gives better sampling so it is frequently used for free energy 
calculations.  You may get comparable results with the leap-frog integrator, but 
I haven never done a side-by-side comparison.


-Justin


I have already done a considerable amount of work using md integration, and
I want to make sure that the free energy values I calculate are consistent
with my previous work.

If using the md integrator is not sound, is there an alternative way of
calculating solvation energy that will be consistent?

Best Regards,

Dan



--
==

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

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Re: [gmx-users] performance issue with many short MD runs

[Mark Abraham]

Hi,

As Peter notes, there are cases where the GPU won't be used for the rerun
(specifically, when you request more than one energy group, for which it
would likely be prohibitively slow, even if we'd write and run such a
kernel on the GPU; but that is not the case here). The reason things take a
long time is that a rerun has a wildly different execution profile from
normal mdrun. Each "step" has to get the positions from some cold part of
memory/disk, do a fresh neighbor search (since mdrun can't rely on the
usual assumption that you can re-use the last one quite a few times),
launch a GPU kernel, launch CPU OpenMP regions, compute forces that often
won't even be used for output, and write whatever should be output. Most of
that code is run very rarely in a normal production simulation, so isn't
heavily optimized. But your rerun is spending most of its time there. Since
you note that your compute load is a single small molecule, it would not be
at all surprising for the mdrun performance breakdown in the log file to
show that all the overheads take very much more time than the GPU kernel
that computes the energy that you want. Those can take wildly different
amounts of time on different machines for all sorts of reasons, including
CUDA API overhead (as Peter noted), Linux kernel configuration, OS version,
hard disk performance, machine load, whether the sysadmin showered lately,
the phase of the moon, etc. :-)

Compare the final sections of the log files to see what I mean. Try gmx
mdrun -rerun -nb cpu, as it might be faster to waste the GPU. If you really
are doing many machine-hours of such jobs and care about turn-around time,
invest human time in writing a script to break up your trajectory into
pieces, and give each piece to a single mdrun that you place on e.g. a
different single core (e.g. with tools like numactl or taskset) and run a
different gmx mdrun -rerun -nb cpu -ntmpi 1 -ntomp 1 on each single core.

Mark

On Mon, Mar 27, 2017 at 4:24 PM Peter Kroon  wrote:

> Hi,
>
>
> On the new machine your CUDA runtime and driver versions are lower than
> on the old machine. Maybe that could explain it? (is the GPU even used
> with -rerun?) You would need to recompile gromacs.
>
>
> Peter
>
>
> On 27-03-17 15:51, Michael Brunsteiner wrote:
> > Hi,I have to run a lot (many thousands) of very short MD reruns with
> gmx.Using gmx-2016.3 it works without problems, however, what i see is
> thatthe overall performance (in terms of REAL execution time as measured
> with the unix time command)which I get on a relatively new computer is
> poorer than what i get with a much older machine
> > (by a factor of about 2 -  this in spite of gmx reporting a better
> performance of the new machine in thelog file)
> >
> > both machines run linux (debian), the old has eight intel cores the
> newer one 12.
> > on the newer machine gmx uses a supposedly faster SIMD instruction
> setotherwise hardware (including hard drives) is comparable.
> >
> > below output of a typical job (gmx mdrun -rerun with a trajectory
> containingnot more than a couple of thousand conformations of a single
> small molecule)on both machines (mdp file content below)
> >
> > old machine:prompt> time gmx mdrun ...
> > in the log file:
> >Core t (s)   Wall t (s)(%)
> >Time:4.5270.566  800.0
> >  (ns/day)(hour/ns)
> > Performance:1.527   15.719
> > on the command line:
> > real2m45.562s  <
> > user15m40.901s
> > sys 0m33.319s
> >
> > new machine:
> > prompt> time gmx mdrun ...
> > in the log file:   Core t (s)   Wall t (s)(%)
> >Time:6.0300.502 1200.0
> >  (ns/day)(hour/ns)
> > Performance:1.719   13.958
> >
> > on the command line:real5m30.962s
> <
> > user20m2.208s
> > sys 3m28.676s
> >
> >  The specs of the two gmx installations are given below.I'd be grateful
> if anyone could suggest ways to improve performanceon the newer machine!
> > cheers,Michael
> >
> >
> > the older machine (here the jobs run faster):  gmx --version
> >
> > GROMACS version:2016.3
> > Precision:  single
> > Memory model:   64 bit
> > MPI library:thread_mpi
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> > GPU support:CUDA
> > SIMD instructions:  SSE4.1
> > FFT library:fftw-3.3.5-sse2
> > RDTSCP usage:   enabled
> > TNG support:enabled
> > Hwloc support:  hwloc-1.8.0
> > Tracing support:disabled
> > Built on:   Tue Mar 21 11:24:42 CET 2017
> > Built by:   root@rcpetemp1 [CMAKE]
> > Build OS/arch:  Linux 3.13.0-79-generic x86_64
> > Build CPU vendor:   Intel
> > Build CPU brand:Intel(R) Core(TM) i7 CPU 960  @ 3.20GHz
> > Build CPU family:   6   Model: 26   Stepping: 5
> > Build CPU features: apic clfsh cmov cx8 cx16 ht

[gmx-users] Unbiased or biased

[m g]

Dear Justin Lemkul,I red your tutorial "Umbrella Sampling", I want to know 
about unbiased and biased method. you sad that used biasing potential. which 
parameter in md files refers to biased? how can i used unbiased method? what is 
difference between unbiased and biased exactly? I used this method that you 
learned in this tutorial for pulling a drug molecule across the POPC membrane, 
but I don't know in my work this PMF is unbiased or biased. would you pleas 
help me?Thanks
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Re: [gmx-users] Gromacs and Radeon Nano

[melichercik]

Hi,
after some suggestions and some dealing with AMD I still don't have the
working solution. Even I don't have any clue for those freezes/crashes.
The double GPU was really mesa and amd driver double checks. I have tried
Ubuntu in 14.4.2, 16.4.1 and 16.4.4 versions (first two should be
supported by AMD), but problem stays without change.
So, please, could you (Szilárd or however has working some Radeon Fury
card) send me the configuration of yours computer (just to compare it). Or
even some your .tpr file which works/or may be I could send you mine to
test (up to 10 minutes - this time is enough for my case to crash in 90%).
I don't know it could influence dual socket configuration (but I don't
have other CPU to (nearly) fully load such powerful card in Gromacs) - at
least not with my calculation tasks.
And BTW which distribution are you using (with working Fury card). I have
tried only Debian/Ubuntu, but I don't thing the using Redhat/CentOS/Suse
would change something.

And the Null pointer dereference of newest AMDGPU-Pro 16.60 in call of
anything with OpenCL (even theirs clinfo) was caused by "ast" module for
onboard graphics - probably they changed something about OpenCL detection
which caused this bug (the older versions works with this kernel module).
Maybe someone find this information useful.

With freezing - with AMDGPU-PRO I was able to measure the temperature and
in state of frozen mdrun the sensors reported temperature of card as 511
deg. C. It is strange, isn't it?

Thanks.

Milan

> Hi,
>
> I have no knowledge of the instability/crash with fglrx; with
> AMDGPU-PRO I have seen strange hangs which *seem* to be kernel-space
> issues because the machine becomes unresponsive for second to minutes
> (but it typically recovers). However, I had no time to investigate
>
> Given that the extensive testing I've done was on fglrx, I'd think
> that's still the most robust choice -- though sadly unsupported and
> outdated (not even sure what's the last kernel it works with?).
>
>
> The fact that your GPU is listed twice is not something I've seen
> myself before, but it's not unreasonable if you have both the mesa and
> the amdgpu-pro OpenCL stacks installed. The former is the open source
> graphics stack + OpenCL compiler which is not fully stable for GROMACS
> use yet (mesa 13.1.x work better, but still not production ready)
>
> When it comes to AMDGPU-PRO issues, I'd strongly recommend trying to
> reach out to AMD support and voice your feedback. Do us know if you
> found a solution!
>
> Cheers,
> --
> Szilárd
>
>
> On Wed, Feb 8, 2017 at 2:23 AM,   wrote:
>> Hi people,
>> I have computer with 2x Xeon E5-2660 with Radeon Fury (as someone here
>> recomended it as quite decent card (not the best one ;-) of course ).
>> System is debian (testing). I have previously R9 280X instead and it
>> worked without problem. After I replaced less power hungry Radeon Fury,
>> it freezes the machine from time to time (but at least one a day) or in
>> better case segfaults gromacs. I tryied latest fglrx (15.12) and all
>> amdgpu-pro (16.40, 16.50 and 16.60) and gromacs (I think) all versions
>> from 5.1 to 2016.2. With exception of latest Amdgpu-pro 16.60 which
>> totaly failed in runing OpenCL-enabled GMX, it gets better in time, but
>> it still crashes. So do have someone any idea wich could help?
>> Thanks in advance.
>>
>> Best,
>>
>> Milan
>>
>> PS: PSU is EVGA Supernova B2 750 W, which should be quite enough (and
>> more hungry R9 280X worked) and it should be quite good PSU (by Tier2 of
>> Tom's Hardware list)
>> PS2: maybe it is not important, but I think I have tested/simulated only
>> .tpr created in older versions of GMX than 2016.x (which I used mostly
>> for simulating)
>> PS3: why is all Radeon GPU using amdgpu-pro detected twice? ()see below)
>> (at least I have tested with Radeon Nano and RX460 cards). And the 2nd
>> one doesn't work, I have to use -gpu_id parameter.
>>
>> Hardware detected:
>>   CPU info:
>> Vendor: Intel
>> Brand:  Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz
>> SIMD instructions most likely to fit this hardware: AVX_256
>> SIMD instructions selected at GROMACS compile time: AVX_256
>>
>>   Hardware topology: Full, with devices
>>   GPU info:
>> Number of GPUs detected: 2
>> #0: name: Fiji, vendor: Advanced Micro Devices, Inc., device
>> version: OpenCL 1.2 AMD-APP (2236.5), stat: compatible
>> #1: name: AMD FIJI (DRM 3.8.0 / 4.9.0-1-amd64, LLVM 3.9.1), vendor:
>> AMD, device version: OpenCL 1.1 Mesa 13.0.3, stat: compatible
>>
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[gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

[spss4]

- Forwarded message from sp...@iacs.res.in -
   Date: Fri, 24 Mar 2017 16:24:21 +0530
   From: sp...@iacs.res.in
Subject: How to calculate Hydrophobic and Hydrophilic SASA separately in
latest version of gromacs?
     To: gmx-us...@gromacs.org

 Hello,
I am a new user of gromacs. I am trying to calculate SASA for a protein
system. I have used the command

 gmx sasa -f traj.trr -s md.tpr -o sasa.xvg -n index.ndx

 From this I can only get the total SASA but I want hydrophobic and
hydrophilic SASA separately. I know it can be done using g_sas command for
older version. But I am using newer version of gromacs (gromacs-2016.1).
Please help me to solve this problem. Thanks in advance.

Sunipa Sarkar

- End forwarded message -
--- Begin Message ---

Hello,
I am a new user of gromacs. I am trying to calculate SASA for a protein
system. I have used the command

 gmx sasa -f traj.trr -s md.tpr -o sasa.xvg -n index.ndx

 From this I can only get the total SASA but I want hydrophobic and
hydrophilic SASA separately. I know it can be done using g_sas command for
older version. But I am using newer version of gromacs (gromacs-2016.1).
Please help me to solve this problem. Thanks in advance.

Sunipa Sarkar
--- End Message ---
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Re: [gmx-users] performance issue with many short MD runs

[Peter Kroon]

Hi,


On the new machine your CUDA runtime and driver versions are lower than
on the old machine. Maybe that could explain it? (is the GPU even used
with -rerun?) You would need to recompile gromacs.


Peter


On 27-03-17 15:51, Michael Brunsteiner wrote:
> Hi,I have to run a lot (many thousands) of very short MD reruns with 
> gmx.Using gmx-2016.3 it works without problems, however, what i see is 
> thatthe overall performance (in terms of REAL execution time as measured with 
> the unix time command)which I get on a relatively new computer is poorer than 
> what i get with a much older machine 
> (by a factor of about 2 -  this in spite of gmx reporting a better 
> performance of the new machine in thelog file)
>
> both machines run linux (debian), the old has eight intel cores the newer one 
> 12. 
> on the newer machine gmx uses a supposedly faster SIMD instruction 
> setotherwise hardware (including hard drives) is comparable.
>
> below output of a typical job (gmx mdrun -rerun with a trajectory 
> containingnot more than a couple of thousand conformations of a single small 
> molecule)on both machines (mdp file content below)
>
> old machine:prompt> time gmx mdrun ...
> in the log file:
>Core t (s)   Wall t (s)(%)
>Time:4.5270.566  800.0
>  (ns/day)(hour/ns)
> Performance:1.527   15.719
> on the command line:
> real2m45.562s  <
> user15m40.901s
> sys 0m33.319s
>
> new machine:
> prompt> time gmx mdrun ...
> in the log file:   Core t (s)   Wall t (s)(%)
>Time:6.0300.502 1200.0
>  (ns/day)(hour/ns)
> Performance:1.719   13.958
>
> on the command line:real5m30.962s  <
> user20m2.208s
> sys 3m28.676s
>
>  The specs of the two gmx installations are given below.I'd be grateful if 
> anyone could suggest ways to improve performanceon the newer machine!
> cheers,Michael
>
>
> the older machine (here the jobs run faster):  gmx --version
>
> GROMACS version:2016.3
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:CUDA
> SIMD instructions:  SSE4.1
> FFT library:fftw-3.3.5-sse2
> RDTSCP usage:   enabled
> TNG support:enabled
> Hwloc support:  hwloc-1.8.0
> Tracing support:disabled
> Built on:   Tue Mar 21 11:24:42 CET 2017
> Built by:   root@rcpetemp1 [CMAKE]
> Build OS/arch:  Linux 3.13.0-79-generic x86_64
> Build CPU vendor:   Intel
> Build CPU brand:Intel(R) Core(TM) i7 CPU 960  @ 3.20GHz
> Build CPU family:   6   Model: 26   Stepping: 5
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc 
> pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> C compiler: /usr/bin/cc GNU 4.8.4
> C compiler flags:-msse4.1 -O3 -DNDEBUG -funroll-all-loops 
> -fexcess-precision=fast  
> C++ compiler:   /usr/bin/c++ GNU 4.8.4
> C++ compiler flags:  -msse4.1-std=c++0x   -O3 -DNDEBUG -funroll-all-loops 
> -fexcess-precision=fast  
> CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
> driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
> Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
> CUDA compiler 
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;;-Xcompiler;,-msse4.1,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,;
>  
> CUDA driver:7.50
> CUDA runtime:   7.50
>
>
>
> the newer machine (here execution is slower by a factor 2):  gmx --version
>
> GROMACS version:2016.3
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:CUDA
> SIMD instructions:  AVX_256
> FFT library:fftw-3.3.5
> RDTSCP usage:   enabled
> TNG support:enabled
> Hwloc support:  hwloc-1.10.0
> Tracing support:disabled
> Built on:   Fri Mar 24 11:18:29 CET 2017
> Built by:   root@rcpe-sbd-node01 [CMAKE]
> Build OS/arch:  Linux 3.14-2-amd64 x86_64
> Build CPU vendor:   Intel
> Build CPU brand:Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
> Build CPU family:   6   Model: 62   Stepping: 4
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf mmx msr 
> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 
> sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /usr/bin/cc GNU 4.9.2
> C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops 
> -fexce

Re: [gmx-users] Lipid water simulation

[Peter Kroon]

Hi,


On 27-03-17 03:55, Sheikh Imamul Hossain wrote:
> Hi all,
>
> I am trying to simulate 1024 dppc lipids with water. I have prepared my
> system using Charmm-Gui monolayer builder. Then I converted the atomistic
> system to coarse grained system using bacdward.py. The box size I got in
> the gro file was 18.246   18.38  23.7. Then I added CG water between the
> two dppc monolayers within the box 18.246   18.384.22. The I increased
> the box size to 18.246  18.3850.00. The total number of CG water is
> 6144. I minimized the system then equilibrated the system three times with
> time steps 2fs, 10fs and 15fs. Then I did the production run for 2
> microsecond using 20fs time steps. The temperature 310K was used in surface
> tension coupling with surface tension 20mN/m per leaflet. I  have few
> questions
>
> 1. After the first equilibration some (very few) CG water found in the air
> space of the box  i.e in the top and bottom of the dppc monolayers. Which
> are supposed to be attached together with other water between the two
> monolayer. Is there any solution to prevent this?
If you're running in an NPT ensemble the pressure coupling should take
care of any air/vacuum bubbles. Depending on how far away from
equilibrium you start this may take a while though.
>
> 2. Is there any other option to build the CG monolayer system and adding CG
> water between the two monolayers? I used gmx solvate to add water.
You can probably also use the insane script to build monolayers (I'm not
sure though). If you have those you can stack them together (with some
space in between) using gmx editconf. You'll probably still need to
solvate it using gmx solvate.
>
> 3. I used 6 CG water per lipid. How many CG water can be added against the
> number of lipids?
Depends on what you want to simulate. If you're using Martini, 1 CG
water = 4 H2O molecules; so you can calculate the concentration of
lipids in water.

Peter
>
> N.B.
>
> After analyzing my system with the help of Bevan Lab DPPC tutorials I got
> the area per lipid 0.5845. I used the formula
> Area per lipid = (Box-X*Box-Y)/ # of lipid per leaflet
>
> Thanks in advance.
>
> Sincerely Your’s
> Sheikh Imamul Hossain
> PhD student at QUT


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[gmx-users] performance issue with many short MD runs

[Michael Brunsteiner]

Hi,I have to run a lot (many thousands) of very short MD reruns with gmx.Using 
gmx-2016.3 it works without problems, however, what i see is thatthe overall 
performance (in terms of REAL execution time as measured with the unix time 
command)which I get on a relatively new computer is poorer than what i get with 
a much older machine 
(by a factor of about 2 -  this in spite of gmx reporting a better performance 
of the new machine in thelog file)

both machines run linux (debian), the old has eight intel cores the newer one 
12. 
on the newer machine gmx uses a supposedly faster SIMD instruction setotherwise 
hardware (including hard drives) is comparable.

below output of a typical job (gmx mdrun -rerun with a trajectory containingnot 
more than a couple of thousand conformations of a single small molecule)on both 
machines (mdp file content below)

old machine:prompt> time gmx mdrun ...
in the log file:
   Core t (s)   Wall t (s)    (%)
   Time:    4.527    0.566  800.0
 (ns/day)    (hour/ns)
Performance:    1.527   15.719
on the command line:
real    2m45.562s  <
user    15m40.901s
sys 0m33.319s

new machine:
prompt> time gmx mdrun ...
in the log file:   Core t (s)   Wall t (s)    (%)
   Time:    6.030    0.502 1200.0
 (ns/day)    (hour/ns)
Performance:    1.719   13.958

on the command line:real    5m30.962s  <
user    20m2.208s
sys 3m28.676s

 The specs of the two gmx installations are given below.I'd be grateful if 
anyone could suggest ways to improve performanceon the newer machine!
cheers,Michael


the older machine (here the jobs run faster):  gmx --version

GROMACS version:    2016.3
Precision:  single
Memory model:   64 bit
MPI library:    thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:    CUDA
SIMD instructions:  SSE4.1
FFT library:    fftw-3.3.5-sse2
RDTSCP usage:   enabled
TNG support:    enabled
Hwloc support:  hwloc-1.8.0
Tracing support:    disabled
Built on:   Tue Mar 21 11:24:42 CET 2017
Built by:   root@rcpetemp1 [CMAKE]
Build OS/arch:  Linux 3.13.0-79-generic x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i7 CPU 960  @ 3.20GHz
Build CPU family:   6   Model: 26   Stepping: 5
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pdcm 
popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
C compiler: /usr/bin/cc GNU 4.8.4
C compiler flags:    -msse4.1 -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
C++ compiler:   /usr/bin/c++ GNU 4.8.4
C++ compiler flags:  -msse4.1    -std=c++0x   -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on 
Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
CUDA compiler 
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;;-Xcompiler;,-msse4.1,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,;
 
CUDA driver:    7.50
CUDA runtime:   7.50



the newer machine (here execution is slower by a factor 2):  gmx --version

GROMACS version:    2016.3
Precision:  single
Memory model:   64 bit
MPI library:    thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:    CUDA
SIMD instructions:  AVX_256
FFT library:    fftw-3.3.5
RDTSCP usage:   enabled
TNG support:    enabled
Hwloc support:  hwloc-1.10.0
Tracing support:    disabled
Built on:   Fri Mar 24 11:18:29 CET 2017
Built by:   root@rcpe-sbd-node01 [CMAKE]
Build OS/arch:  Linux 3.14-2-amd64 x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
Build CPU family:   6   Model: 62   Stepping: 4
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.9.2
C compiler flags:    -mavx -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
C++ compiler:   /usr/bin/c++ GNU 4.9.2
C++ compiler flags:  -mavx    -std=c++0x   -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
CUDA compiler:  /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on 
Wed_Jul_17_18:36:13_PDT_2013;Cuda compilation tools, release 5.5, V5.5.0
CUDA compiler 
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-ge

[gmx-users] Extracting Energy of Individual Molecules From Energy File

[Kelechi Okoroafor]

Hello, All.

Please is it possible to extract the different components of energy (i.e.
Bond, Angle, Coulombic and LJ) for individual molecule from the *.edr file?

-- 
Best wishes,
Kelechi
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Re: [gmx-users] PMF - US histograms problem

[Sajeewa Pemasinghe]

Hi,

When I get  a region sparsely populated like that, I increase the number of
points in that particular region and increase the k value to about 3000 but
not more than that. Increasing the k value to something like 2 will
result in the distribution getting very narrow and therefore further
hindering the overlap. It could also be that the coordinate(path) you have
chosen is not a good one to pull the peptide out. Changing the
pull_geometry from distance to cylinder might also help as used in this
article.

http://www.cell.com/biophysj/fulltext/S0006-3495(12)01180-0

Best,

Sajeewa



On Mon, Mar 27, 2017 at 1:50 PM, Eudes Fileti  wrote:

> Hi everyone, I'm trying to calculate the PMF for the extraction of a
> peptide from within a peptide nanostructure. However I'm having difficulty
> to overlap the histograms for the first pulling windows: Many full overlap
> windows follow by a large gap with no histogram.
>
> I've tried the two things I could: reduce the distance increment between
> the windows (now I'm using 0.05nm), and I've already done several tests
> with different force constants with k up to 2! For each window test I
> run only 1ns of sampling.
>
> Anyone have any suggestions? Could another umbrella sampling scheme
> (constraint pulling) be more efficient in this case?
>
> Bests
> ___
> Eudes Eterno Fileti
> Instituto de Ciência e Tecnologia da UNIFESP
> Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014
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Re: [gmx-users] Regarding Glycine structure

[Dilip H N]

Thanks Justin,

But my doubts are..
1] after energy minimization of both glycine non zwitterionic form and
zwitterionic form with water, if i visualize it in vmd, the bond between
some of the water molecules are broken.. why is this so..??
2] and ran nvt,npt,md simulations respectively...and during analysis part i
am getting only similar two types of RDF graphs...why is this happening...i
have made all the indexing, etc., proper...

Is there any tutorials for these as an example..?? solving this would help
me a lot


   Sent with Mailtrack


On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  wrote:

>
>
> On 3/23/17 2:05 PM, Dilip H N wrote:
>
>> Hello,
>>
>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in
>> the first step if i do the energy minimization and then visualizes the
>> mixture, the glycine is no more in its pure form as before instead it has
>> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
>> bonds with water are also broken. How can i solve these both issues..??
>>
>>
> Glycine didn't convert between forms.  That's impossible; bonds can't
> break or form in a molecular mechanical process.  The termini are exactly
> what you assigned them to be.  If you want them to be something else, you
> have to assign them as such with pdb2gmx.  Though you should note that NH2
> and COOH can't coincide at any real pH value.
>
> -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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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Restraining Protein-ligand distance

[Juan José Galano Frutos]

Hi there,

I am trying AFEC simulations in complex (ligand-protein), but sometimes I
get the ligands out the binding site, but I dont want that scenary. I was
thinking the situation of applying distance retraints between a ligand and
a protein was already solved in GROMACS version later 5.0... without any
necessity of making a hybrid system. But, I'm using version 5.1, and it
seems that's not possible doing so, because I'm obtaining errors.
Is there currently any happy solution to restraint ligand-protein distance?
or Has one to still go through the unbrella pulling option to do that?

In the case I need to do a hybrid system what would be a good procedure?

Thank you very much.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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[gmx-users] solvate with hexagonal box

[Erik Marklund]

Dear gmx-users,

We are trying to merge a box containing a peripheral membrane protein with 
another box generated with memgen. Both boxes are hexagonal and exactly the 
same size,Naively, we thought that gmx solvate -cp protein.gro -cs 
membrane_and_water.gro would do the trick. Unfortunately, this causes gmx 
solvate to crash:

Generating solvent configuration
Will generate new solvent configuration of 1x2x1 boxes
Solvent box contains 99373 atoms in 28208 residues
Removed 12253 solvent atoms due to solvent-solvent overlap
Removed 5122 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 2 different molecule types:
   POPE (  52 atoms):   233 residues
SOL (   3 atoms): 23294 residues
gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0: pointer 
being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

So we then tried to remove the membrane, keeping only the water, and use that 
system as the argument for -cs. Gmx solvate doesn’t crash now, but the output 
file has strange gaps of some size in the water parts, which cannot be 
explained by the removed lipids. Can gmx solvate not handle non-orthogonal 
boxes as arguments for -cs?

The whole point in doing it this way was to avoid water molecules being 
inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad 
things went with gmx solvate.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

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[gmx-users] forcefield installation on GROMACS 5.1.4

[Simon Kit Sang Chu]

Hi everyone,

Recently I am looking into PACE
 for my system and
installation of forcefield is required. The files located inside the
forcefield directory is given by -

aminoacids.rtp  cgWater.itp  ffPACE_1.3-c.tdb  ffPACE_1.3.hdb
 ffPACE_1.3-n.tdb
cg216water.gro  ffPACE_1.3.atp  ffPACE_1.3.ddbffPACE_1.3.itp
 ffPACE_1.3.rtp

Compared to the standard forcefields, such as CHARMM and AMBER, there is no
.doc. I located these files in
/usr/local/gromacs/share/gromacs/top/PACE_1.3.ff.

When I tried to implement the forcefield with pdb2gmx, I see no sign of
PACE and option -ff returns error too.

I am new to GROMACS. Would anyone suggest any solution or references that I
should look into?

Thank you.
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Re: [gmx-users] Secondary structure analysis

[RAHUL SURESH]

i found a lot libraries missing in dssp.

can i obtain them using
*rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ 
/home/oem/Downloads/dssp*

On Sun, Mar 26, 2017 at 9:44 PM, Souparno Adhikary 
wrote:

> I think dssp is a useful tool for this purpose...
>
> Souparno
>
> On 26 Mar 2017 19:50, "Justin Lemkul"  wrote:
>
> >
> >
> > On 3/26/17 8:21 AM, RAHUL SURESH wrote:
> >
> >> I use gromacs 2016.1 version. How to do secondary structure analysis ?
> >>
> >>
> > http://manual.gromacs.org/documentation/2016.1/user-guide/
> > cmdline.html#protein-specific-analysis
> >
> > -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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] PMF - US histograms problem

[Eudes Fileti]

Hi everyone, I'm trying to calculate the PMF for the extraction of a
peptide from within a peptide nanostructure. However I'm having difficulty
to overlap the histograms for the first pulling windows: Many full overlap
windows follow by a large gap with no histogram.

I've tried the two things I could: reduce the distance increment between
the windows (now I'm using 0.05nm), and I've already done several tests
with different force constants with k up to 2! For each window test I
run only 1ns of sampling.

Anyone have any suggestions? Could another umbrella sampling scheme
(constraint pulling) be more efficient in this case?

Bests
___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014
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Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

[masoud keramati]

Hi
They have a web site and all of things you need is there:
http://rashmikumari.github.io/g_mmpbsa/

On Mar 27, 2017 10:15 AM, "Neha Gupta"  wrote:

> Hi gromacs users,
>
> How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of
> amber software package?
>
>
> Thanks,
> Neha
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