date:20170731

On 7/31/17 5:19 PM, Yuanchao Liu (MSU) wrote:

Hi all

Here is some detail of my simulation:
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMCVXRkp3tPYrhq-5F4oRHdtfnRb1VJo71U0_=DwIFaQ=nE__W8dFE-shTxStwXtp0A=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess=B67nP5cwU6r5g_KBORUyrzAardEsfEzcojVKVZFomfU=

I will appreciate it if anybody with relevant experience can give me some
suggestion on this. Thank you.

It will be difficult to determine any real, meaningful difference with such
small changes in ionic strength. Your histogram overlap looks good, so I doubt
that more sampling will improve the result. Is the observed difference in
retention time reproducible? How did you determine it, and over what time
scale? Is it possible that those simulations simply got stuck in a local
minimum (common in MD simulations) rather than actually reflecting a real
physical difference? Additionally, if the retention times are not substantially
different, then the energy differences may not be large enough to resolve via
umbrella sampling.

-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] How can I implement a radial potential field in GROMACS?

On 7/31/17 1:07 PM, Wes Michaels wrote:

Hello,

(Cross-post from my original post here:
https://www.researchgate.net/post/How_can_I_implement_a_radial_potential_field_in_a_MD_simulation_GROMACS)

Is there a way to apply a potential field to all atoms in a simulation box in
GROMACS? I'd like to implement some radial potential energy function, such as
U(r)=k*r^2 or similar, that applies a force to each atom as a function of its
position. In my case, I’d like to draw atoms towards the center of the box.

I looked into implementing this with the pull code with a dummy atom, but I
gathered that the pull code acts on the center of mass of the specified index
group, not on each atom in the group. So, if all the atoms in my simulation in
a given index group are distributed radially around the center of my box, no
force will be applied. Scaling behavior of Coulomb and LJ potentials on the
dummy atom seems to rule them out as possible sources of a potential, too.

Is there a way I can modify the reference positions of position restraints of
atoms to be centered at the middle of the box, instead of the atom's initial
position? Or, can I implement a solution using force switching that acts only
on the dummy atom? Or, is there another way to tackle this problem?

Thanks! Any and all suggestions are appreciated. If clarification is needed on
my desired goal, just let me know.

It seems to me that you can do this with a simple use of position restraints on
all atoms, with a reference position set for each at the middle of the box via
grompp -r.

-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] gromacs rerun calculate the energy




On 7/31/17 8:03 AM, 王珍 wrote:

Hi all,
   I used Gromacs run the biological system,  which contains water, 
ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype 
was PME and the cutoff was 10 angstrom,  then I want to use the commond rerun 
to calculate the interaction of resid 1 and resid 2, I add the energygrps in my 
mdp, and the coulombtype was PME, the .edr file can be obtained. Then I use 
g_energy to calculate the coulomb interaction. I have three question.
first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10 angstrom, 
is PME algorithm using ?



Yes, because there are both real-space (within rcoulomb) and Fourier space 
(long-range) terms.





second, The PME algorithm dived into long range interaction and short range 
interaction, whereas we only calculate the short range of the coulomb energy 
using Gromacs, can we obtain the long range of the coulomb energy?



Perhaps by clever use of convert-tpr to zero out charges of certain groups 
(there is a post in the archive from some time ago about this) but I am 
skeptical about the value of such a number.





Third, when I use rerun to calculate the coulomb energy, the rcoulomb from 1.0 
nanometre change to half of the water box I built, and the coulombtype from PME 
to cut-off, is it reasonable to calculate the coulomb energy?



This is probably the more straightforward way to determine a reasonable estimate 
of the longer-range energy contributions.


-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] gmx mdmat calculation of heavy atoms of two side chains




On 7/31/17 1:19 AM, Мижээ Батсайхан wrote:

Dear gmx users,

I would like to know about the hydrophobic interaction between heavy atoms
of side chains in different chains of peptides. How can I use mdmat tool
for this calculation? I  separately indexed all heavy atoms but mdmat use
only one index group in the calculation. I re-integrated all separate
groups into a group. Calculation result came out only two side chain
distance image.


A single, merged group is the proper approach.  This is the only way to get a 
matrix of all (NxN) atomic interactions.


-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] hole in the simulation box

2017-07-31 Thread Dallas Warren

There are insufficient waters in the box to fill it up completely.

Two solutions that come to mind, add more water so it reaches the
appropriate simulated density under those conditions, or run under NPT
until reaches appropriate simulated density then swap back to NVT.
Catch ya,

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

On 31 July 2017 at 18:14, edesantis  wrote:
> Hi gromacs users,
>
> I am trying to simulate a crystal supershell (5x5x5 unit cells) with martini
> ff in gromacs 5.
>
> I build the system in aa representation, then I converted it in CG using the
> martinize.py script,
>
> following the tutorial, I've done a brief equilibration in water, the after
> the solvatation of the system with non-polarizable water, I've perform
> another energy minimization followed by the equilibration.
>
> then I've performed md simulation in the NVT ensemble.
>
> It happened that during the first steps of md, an empty (no protein no
> water) hole was created in my simulation box. during the md simulation the
> hole size became bigger (this hole doesn't appear if I do the simulation in
> NPT, but I'd prefer to avoid this ensemble since a dynamic volume of the box
> could alter the reticolar parameters of my crystal),
>
> I've tried to calculate forces using different algorithms but the hole is
> formed every time.
>
> the density of my system is 1.1 times the experimental one.
>
> Do you have an idea of the reason why I found this hole? do you have any
> suggestion to avoid its formation??
>
>
> thank you in advance,
> regards
> Emiliano De Santis
>
> --
> Emiliano De Santis
> --
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[gmx-users] Question on Umbrella Sampling with varied ionic strength.

2017-07-31 Thread Yuanchao Liu (MSU)

Hi all

Here is some detail of my simulation:
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMCVXRkp3tPYrhq-5F4oRHdtfnRb1VJo71U0_=DwIFaQ=nE__W8dFE-shTxStwXtp0A=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess=B67nP5cwU6r5g_KBORUyrzAardEsfEzcojVKVZFomfU=

I will appreciate it if anybody with relevant experience can give me some
suggestion on this. Thank you.

Yuanchao Liu (刘元超)
Ph.D. Candidate
Department of Chemical Engineering and Materials Science
428 South Shaw Lane, Room 3263
Michigan State University
East Lansing, Michigan 48824-4437

Email: ycliu1...@gmail.com; liuyu...@msu.edu; liuyu...@egr.msu.edu
Cell:+1 (517)-763-1806
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hi,

Did you get any warnings from grompp?

Mark

On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:

> Hello GROMACS users,
>
> I'm doing MD for nitrogen, and for better electrostatic interactions I need
> to use massless and charged virtual site. I did that but when I try to do
> energy minimization gives me LINCS warning and crush. I don't know where is
> the error I tried a lot but could not find a solution.
> Anyone has an idea where is my error
>
> Here is the topology file (hand written)
>
> --
>
> [ defaults ]
>
> 1 3 yes 0.5 0.5
>
> ;
>
> [ atomtypes ]
>
> ; name  bond_typemasscharge   ptype  sigma  epsilon
>
>   OP   OP0.000   0.000A  0.330  0.3062 ;
> nitrogen
>
>   M  M  0.000   0.000V  0.000  0.000 ;
> virtual site
>
>
> 
>
> [ moleculetype ]
>
> ; name  nrexcl
>
> N2 2
>
>
>
> [ atoms ]
>
> ;   nr   typeresnr residue  atom   cgnr   charge mass
>
>  1 OP  1N2 N1  1-0.482  14.0067
>
>  2 M 1N2 M1  1 0.964 0.000
>
>  3 OP   1N2 N2  1-0.482 14.0067
>
>
>
> [ constraints ]
>
> ; the N-N is fixed
>
> 1   3   1   0.11
>
>
>
> [ virtual_sites2 ]
>
> ; site  ai  aj  funct   a
>
>  2   1   3  1   0.5000  ; right in the mid
>
>
>
> 
>
> [ system ]
>
> N2 in vacuo
>
>
>
> [ molecules ]
>
> N2 1500
>
> 
> --
>
> Here is the structure (N2.pdb)
>
> ---
>
> TITLE N2 with dummy masses
>
> REMARKTHIS IS A SIMULATION BOX
>
> MODEL1
>
> COMPNDUNNAMED
>
> AUTHORGENERATED BY OPEN BABEL 2.3.2
>
> CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
>
> ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> 0.00   N
>
> ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> 0.00  Xx
>
> ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> 0.00   N
>
> CONECT13
>
> CONECT31
>
> MASTER000000003030
>
> END0
>
> 
> -
> Thank you
> --
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[gmx-users] Hyper-threading on multi-CPU xeon worstation

2017-07-31 Thread Gleb Novikov

Dear Gromacs users!
I wonder to ask whether is possible to expect an increase in Gromacs 
performance with HT technology on my Xeon cpu (72 cpus without HT and 144 with 
HT)? How would be better to calibrate mdp options  (e.g integrator, adjust 
electrostatics cut-offs) to obtain best performance from my workstation with 
enabled HT? Does the HT give better performance in case of simulation of big 
systems (e.g MARTINI  with  > 200 of CG particles)?

Thanks in advance!
Gleb
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[gmx-users] ligand topology

2017-07-31 Thread Mohammad Zahidul Hossain Khan

Dear Sir

I am new for protein-ligand complex. I want amber force field (ff03) for my
protein, tip3p for water model and gaff (General Amber force field) for
ligand. I do not know how to produce gaff force field from pdb and then
convert for gromacs topology.

I have tried ff03 with gromos ligand topology and tip3p water model

it gives me the error:
atomtype OM not found

and when I have tried ff03 with gromos topology and spc water model it
gives me the error like:
atomtype HW not found.

Can anyone help me about it?

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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[gmx-users] How can I implement a radial potential field in GROMACS?

2017-07-31 Thread Wes Michaels

Hello,

(Cross-post from my original post here: 
https://www.researchgate.net/post/How_can_I_implement_a_radial_potential_field_in_a_MD_simulation_GROMACS)

Is there a way to apply a potential field to all atoms in a simulation box in 
GROMACS? I'd like to implement some radial potential energy function, such as 
U(r)=k*r^2 or similar, that applies a force to each atom as a function of its 
position. In my case, I’d like to draw atoms towards the center of the box.

I looked into implementing this with the pull code with a dummy atom, but I 
gathered that the pull code acts on the center of mass of the specified index 
group, not on each atom in the group. So, if all the atoms in my simulation in 
a given index group are distributed radially around the center of my box, no 
force will be applied. Scaling behavior of Coulomb and LJ potentials on the 
dummy atom seems to rule them out as possible sources of a potential, too.

Is there a way I can modify the reference positions of position restraints of 
atoms to be centered at the middle of the box, instead of the atom's initial 
position? Or, can I implement a solution using force switching that acts only 
on the dummy atom? Or, is there another way to tackle this problem?

Thanks! Any and all suggestions are appreciated. If clarification is needed on 
my desired goal, just let me know.

-Wes



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[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-07-31 Thread Ali Ahmed

Hello GROMACS users,

I'm doing MD for nitrogen, and for better electrostatic interactions I need
to use massless and charged virtual site. I did that but when I try to do
energy minimization gives me LINCS warning and crush. I don't know where is
the error I tried a lot but could not find a solution.
Anyone has an idea where is my error

Here is the topology file (hand written)

--

[ defaults ]

1 3 yes 0.5 0.5

;

[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma  epsilon

  OP   OP0.000   0.000A  0.330  0.3062 ;
nitrogen

  M  M  0.000   0.000V  0.000  0.000 ;
virtual site



[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

 1 OP  1N2 N1  1-0.482  14.0067

 2 M 1N2 M1  1 0.964 0.000

 3 OP   1N2 N2  1-0.482 14.0067



[ constraints ]

; the N-N is fixed

1   3   1   0.11



[ virtual_sites2 ]

; site  ai  aj  funct   a

 2   1   3  1   0.5000  ; right in the mid





[ system ]

N2 in vacuo



[ molecules ]

N2 1500


--

Here is the structure (N2.pdb)

---

TITLE N2 with dummy masses

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1

ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
0.00   N

ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
0.00  Xx

ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
0.00   N

CONECT13

CONECT31

MASTER000000003030

END0


-
Thank you
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Re: [gmx-users] Error in pdb2gmx

Hi,

Google knows that better than I ;-)

Mark

On Mon, 31 Jul 2017 17:11 Souvik Dey  wrote:

> Can you name some of these softwares? I am relatively new in this.
>
> On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You need to build in the residue in a way that makes sense. Using some
> > other software, but there are some suggestions on the Gromacs website.
> >
> > Mark
> >
> > On Mon, 31 Jul 2017 16:57 Souvik Dey  wrote:
> >
> > > Hi,
> > >
> > > I am trying to run pdb2gmx on a long Amino Acid chain. However, one of
> > the
> > > residues in the middle is incomplete. If I change the residue manually
> > > myself, would there be any problem in connectivity? Else, how do I sort
> > out
> > > this problem?
> > >
> > > Souvik
> > >
> > > --
> > > Souvik Dey
> > > Integrated Science Education & Research Centre
> > > Visva Bharati University
> > > Santiniketan-731235
> > > West Bengal
> > > 8981736643
> > > --
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> >
>
>
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
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Re: [gmx-users] Error in pdb2gmx

2017-07-31 Thread Souvik Dey

Can you name some of these softwares? I am relatively new in this.

On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham 
wrote:

> Hi,
>
> You need to build in the residue in a way that makes sense. Using some
> other software, but there are some suggestions on the Gromacs website.
>
> Mark
>
> On Mon, 31 Jul 2017 16:57 Souvik Dey  wrote:
>
> > Hi,
> >
> > I am trying to run pdb2gmx on a long Amino Acid chain. However, one of
> the
> > residues in the middle is incomplete. If I change the residue manually
> > myself, would there be any problem in connectivity? Else, how do I sort
> out
> > this problem?
> >
> > Souvik
> >
> > --
> > Souvik Dey
> > Integrated Science Education & Research Centre
> > Visva Bharati University
> > Santiniketan-731235
> > West Bengal
> > 8981736643
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
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-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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Re: [gmx-users] multiple cpu for g_membed job?

2017-07-31 Thread Albert


oh, I see.

thx a lot


On 07/31/2017 04:48 PM, Mark Abraham wrote:

Hi,

Only one rank, but I believe it works with the Verlet scheme and thus
openmp and a single GPU.

Mark


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Re: [gmx-users] Error in pdb2gmx

Hi,

You need to build in the residue in a way that makes sense. Using some
other software, but there are some suggestions on the Gromacs website.

Mark

On Mon, 31 Jul 2017 16:57 Souvik Dey  wrote:

> Hi,
>
> I am trying to run pdb2gmx on a long Amino Acid chain. However, one of the
> residues in the middle is incomplete. If I change the residue manually
> myself, would there be any problem in connectivity? Else, how do I sort out
> this problem?
>
> Souvik
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
> --
> 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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[gmx-users] Error in pdb2gmx

2017-07-31 Thread Souvik Dey

Hi,

I am trying to run pdb2gmx on a long Amino Acid chain. However, one of the
residues in the middle is incomplete. If I change the residue manually
myself, would there be any problem in connectivity? Else, how do I sort out
this problem?

Souvik

-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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Re: [gmx-users] multiple cpu for g_membed job?

Hi,

Only one rank, but I believe it works with the Verlet scheme and thus
openmp and a single GPU.

Mark

On Mon, 31 Jul 2017 16:44 Albert  wrote:

> Hi guys,
>
> Does anybody know whether g_membed support parallel running using
> multiple CPU for a single job?
>
> thanks a lot
>
> Albert
>
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[gmx-users] multiple cpu for g_membed job?

2017-07-31 Thread Albert


Hi guys,

Does anybody know whether g_membed support parallel running using 
multiple CPU for a single job?


thanks a lot

Albert

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[gmx-users] gromacs rerun calculate the energy

2017-07-31 Thread ????

Hi all,
  I used Gromacs run the biological system,  which contains water, 
ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype 
was PME and the cutoff was 10 angstrom,  then I want to use the commond rerun 
to calculate the interaction of resid 1 and resid 2, I add the energygrps in my 
mdp, and the coulombtype was PME, the .edr file can be obtained. Then I use 
g_energy to calculate the coulomb interaction. I have three question.
first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10 angstrom, 
is PME algorithm using ?



second, The PME algorithm dived into long range interaction and short range 
interaction, whereas we only calculate the short range of the coulomb energy 
using Gromacs, can we obtain the long range of the coulomb energy? 



Third, when I use rerun to calculate the coulomb energy, the rcoulomb from 1.0 
nanometre change to half of the water box I built, and the coulombtype from PME 
to cut-off, is it reasonable to calculate the coulomb energy?


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Re: [gmx-users] Creating Custom .rtp files

2017-07-31 Thread Momin Ahmad


Hello,

the .rtp file is located in the same directory as the force-field. When 
i type gmx gmx2pdb . then the log shows that the right path is 
considered and loads the needed .rtp fiels that already exist in the 
forc-field file. But my custom one is ignored.


Greets
Momin Ahmad

Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:

On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad  wrote:


Hi,

I created a custom .pdb file and the associated .rtp file for the
force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the
5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
version is a local installation in my /home/user folder. The log shows
the correct paths but does not consider my custom .rtp file.

I would recommend to check whether the rtp file location and source where
gmx  you have installed match. Apart from that I do not think any error
with version of Gromacs.


Am i doing
something wrong with the newer version? I added two simple files of my
problem. Thanks in advance.

Cheers
Momin Ahmad
Karlsruher Institut of Technology
Germany
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Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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[gmx-users] Number of Clusters during my simulation

2017-07-31 Thread Pandya, Akash

Hi all,

I want to calculate the number of clusters of my glycine molecules during the 
course of my simulation. I have read that gmx clustsize is the correct command 
to use. I read on one of the previous threads that I will have create a 
separate tpr file for the molecule of interest. And I had to generate another 
trajectory file in order for them to match.  I run the command below:


gmx clustsize -f glycine.xtc -s glycine.tpr -nc nclust.xvg -b 0 -e 6 -cut 
0.35 -mol


I get an error message saying that gromacs only finds 1 cluster but this cannot 
be right as I see more than one cluster forming during the simulation


Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

Can somebody please advise me on how to overcome this issue?


Many thanks,

Akash
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[gmx-users] Configuration of new HPC Cluster for GROMACS and NAMD

2017-07-31 Thread Vogel, Alexander

Hello everybody,

I'm currently highly involved in the planning of a new HPC cluster for MD 
simulations. The main applications are GROMACS (sometimes in conjuction with 
PLUMED) and NAMD. Typical simulations are about 100,000 atoms up to 300,000 at 
max. So we got a quote from a manufacturer and I have a few questions regarding 
the details that probably can only be answered with some experience...and 
that's why I'm asking here:

1. The compute nodes contain 2x Intel Xeon Broadwell-EP E5-2680v4 (each 14 
cores, 2.4GHz base clock) and 8x GTX 1080 Ti. That is very GPU focused and it 
is difficult to find GPU benchmarks of recent GROMACS versions. I found this 
one from Nvidia which seems to suggest that it only scales well up to two GPUs: 
https://www.nvidia.com/object/gromacs-benchmarks.html It is rather likely that 
we will end up using AMD EPYC CPUs once they are out so that we probably will 
have more cores, more PCIe lanes, and a higher memory bandwidth in the end. But 
even in that case 8 GPUs seem too many to me. What do you think?

2. I know this is a GROMACS mailing list but if someone happens to know NAMD 
well: The same question as above just for NAMD. From what I read in the NAMD 
2.13 release notes using many GPUs might make sense because almost everything 
seems to be offloaded to the GPU now and the CPU load has been reduced 
dramatically: "GPU-accelerated simulations less limited by CPU performance. 
Contributed by Antti-Pekka Hynninen. Bonded forces and exclusions are now 
offloaded to the GPU by default. (May be disabled with "bondedCUDA 0". Note 
that this is a bit flag so default is "bondedCUDA 255"; setting "bondedCUDA 1" 
will offload only bonds, not angles, dihedrals, etc.) Removes all load-balanced 
work from the CPU, leaving only integration and optional features. The only 
benefit is for machines that were limited by CPU performance, so a high-end 
dual-socket workstation with an older GPU may see no benefit, while a 
single-socket desktop with the latest 1080 Ti will see the most."

3. Currently the quote contains Infiniband. However, given the computational 
power of a single node (even if just 2 GPUs are used) I could imagine that the 
simulation (which will not be excessive in size...we only plan to use 
simulations up to 300,000 atoms) would not scale well to two nodes or even 
more. If this is the case we could drop Infiniband and invest the money into 
more nodes. What do you think about this?

4. Currently the quote contains 64GB of RAM for each compute node. To me that 
seems very high as from my experience MD simulations only take up a few GB at 
most for "reasonable" system sizes (we only plan to use simulations up to 
300,000 atoms). Using 32GB instead could also save some money. But I don't know 
about PLUMED...maybe that needs more RAM? What do you think about this?

Any help would be highly appreciated,

Alexander

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[gmx-users] Strange acceleration behaviour after continuation

2017-07-31 Thread Kamps, M.

Dear GMX users,

I am trying to replicate a molecular flow of small molecules between
two solid slabs of FCC bound atoms. The slabs are bound via LJ
interactions.The flow is created by using periodicity, where the fluid
is accelerated continuously between the two slabs. The periodic box is
created as a long small 'channel', where periodicity can occur within
the X and Y directions. The Z direction is restricted due to the fixed
'walls'.

I am now trying to control the fluid flow, by altering the
accelerations. To do this, I first accelerate the fluid with a
constant acceleration 'a1'. This will result in a movement of the
fluid over time. At t=0 the velocity is zero, while at t=1 the
velocity equals 0.06 nm/ps2. The velocity development is linear,
meaning it has a linear increase from 0 to this value of 0.06 nm/ps2.

After this 'first stage', I want a less rigorous increase within the
velocity, therefore I perform a second simulation, continued from the
previous simulation. In this case the acceleration is set to a value
that is 20% that of 'a1' (the previous acceleration). Within the MDP
file it is set to genvel=no and continuation=yes. The .cpt and .gro
files are provided as the input for this second simulation.

My expectation is that the velocities at the beginning of this
simulation are equal to that of previous simulation, hence the
continuation. However, this is not the case. The velocities at the
beginning of this simulation start at roughly 0.02 nm/ps2 and increase
(slowly) to 0.04 nm/ps.

My question: why is there a mismatch in the velocities? Am I doing
something wrong? Is my logic flawed?

Mark
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[gmx-users] Calculate RMSD between snapshots of two trajectories

2017-07-31 Thread Dawid das

Dear Gromacs Users,

I would like to get a simple plot of RMSD versus time for two trajectories
in *.gro
format, where RMSD is calculated between structures at the same time, i.e.
snap11 - snap12
snap21 - snap22
snap31 - snap32
snap41 - snap42
.
.
.
where snap31 means third snapshot of the first trajectory. I have run
gmx rms   -s   npt-md2.tpr   -f   traj1.gro   -f2   traj2.gro   -n
index.ndx-mrmsd-small-superlarge.xpm

command and after converting the .xpm file to .eps I can see the
graphical representation of the matrix. However, I would rather see just
RMSD vs time plot as I explained above. How can I do it?

Best wishes,
Dawid Grabarek
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Re: [gmx-users] Nucleic Acid in GROMOS54A7

DA is the Adenine residue. It goes fine with other forcefields like
CHARMM27 and AMBER99 SBILDN. In my knowledge, there's no problem in the
parameters.

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

On Mon, Jul 31, 2017 at 3:43 PM, Mark Abraham 
wrote:

> What is DA, and from your background knowledge of this force field, does it
> have suitable parameters or topologies for DA?
>
> Mark
>
> On Mon, 31 Jul 2017 11:02 Souparno Adhikary  wrote:
>
> > Hi all,
> >
> > I was trying to simulate a protein-DNA complex using gromos54a7
> forcefield.
> > The error comes as,
> >
> > Fatal error:
> > Residue 'DA' not found in residue topology database
> >
> > Clearly, it is not finding the DA residue in its database. How can I
> solve
> > this?
> >
> > Thanks,
> >
> > Souparno Adhikary,
> > CHPC Lab,
> > Department of Microbiology,
> > University of Calcutta.
> > --
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Re: [gmx-users] Nucleic Acid in GROMOS54A7

What is DA, and from your background knowledge of this force field, does it
have suitable parameters or topologies for DA?

Mark

On Mon, 31 Jul 2017 11:02 Souparno Adhikary  wrote:

> Hi all,
>
> I was trying to simulate a protein-DNA complex using gromos54a7 forcefield.
> The error comes as,
>
> Fatal error:
> Residue 'DA' not found in residue topology database
>
> Clearly, it is not finding the DA residue in its database. How can I solve
> this?
>
> Thanks,
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
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Re: [gmx-users] Using external force field with GROMACS

Hi,

I don't understand your description of the problem, but you don't need to
do anything with gmxlib in order to follow my solution, so make your life
easy and do that.

Mark

On Mon, 31 Jul 2017 10:36 Souparno Adhikary  wrote:

> Hi,
>
> There's a new problem. Sysadmins installed the GROMACS 5.1.4 as a module in
> the cluster. We need to load it everytime we login as "module load
> gromacs-5.1.4". Now, if I mention GMXLIB path to the new forcefield files,
> the previous default installation of gromacs (4.5.6) points to it.
>
> How can we specifically mention GROMACS 5.1.4 to work with the new
> forcefield files?
>
> Thanks,
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Fri, Jul 28, 2017 at 2:29 PM, Qinghua Liao 
> wrote:
>
> > Hello,
> >
> > You can also set the variable of GMXLIB so that pdb2gmx can find the
> force
> > field you want to use, like:
> > GMXLIB=/ path /charmm36m.ff
> >
> >
> > Best,
> > Qinghua
> >
> >
> > On 07/28/2017 10:53 AM, Souparno Adhikary wrote:
> >
> >> Hi,
> >>
> >> I want to use the latest CHARMM36m force field which I downloaded from
> >> MacKerell group's website. I use a common HPC system and do not have an
> >> administrator account.
> >>
> >> Can you give me an idea how I can add this forcefield to the pdb2gmx
> >> options? We are using quite an old version of GROMACS- 4.5.6 (I don't
> know
> >> why they are not eager to update it).
> >>
> >> Thanks,
> >>
> >> Souparno Adhikary,
> >> CHPC Lab,
> >> Department of Microbiology,
> >> University of Calcutta.
> >>
> >
> > --
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[gmx-users] Nucleic Acid in GROMOS54A7

Hi all,

I was trying to simulate a protein-DNA complex using gromos54a7 forcefield.
The error comes as,

Fatal error:
Residue 'DA' not found in residue topology database

Clearly, it is not finding the DA residue in its database. How can I solve
this?

Thanks,

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.
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[gmx-users] (no subject)

Hi all,

I was trying to simulate a protein-DNA complex using gromos54a7 forcefield.
The error comes as,

Fatal error:
Residue 'DA' not found in residue topology database

Clearly, it is not finding the DA residue in its database. How can I solve
this?

Thanks,

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.
-- 
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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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 125

2017-07-31 Thread suniba shuaib

*Hi all,>> I am calculating the RDF from a particular residue to a
particular> glycine molecule. I created an index file for both to do this.
My> simulation box is 1.5nm, but the RDF values are in the range of
2nm-3nm.> I have viewed my trajectory and all the components stay inside
the box.> Please could someone tell me how to overcome this issue? My
command line> is below:>> gmx rdf -f output.xtc -s input.tpr -n index.ndx
-o rdf.xvg -b 0 -e 6> -ref -sel -bin 0.5 -norm rdf>> Akash> --*

*Hi *
*Akash*
*Are you sure your simulation box is 1.5 nm? This sounds bit strange and
too small. What is the length of your protein or no. of amino acids. I am
afraid you are talking about the distance from edge to protein is 1.5nm. *

*Regards*
*Suniba*

On Mon, Jul 31, 2017 at 1:58 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>1. Re: Question on force field (YanhuaOuyang)
>2. gmx mdmat calculation of heavy atoms of two side chains
>   (? ?)
>3. RDF Values (Pandya, Akash)
>4. Re: RDF Values (saima kalsoom)
>5. hole in the simulation box (edesantis)
>6. Re: RDF Values (sp...@iacs.res.in)
>
>
> --
>
> Message: 1
> Date: Mon, 31 Jul 2017 10:54:37 +0800 (CST)
> From: YanhuaOuyang <15901283...@163.com>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Question on force field
> Message-ID: <18244f50.3a1e.15d969118bb.coremail.15901283...@163.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Justin,  Thank you very much. I get it now.Best
> regards,Ouyang
> At 2017-07-31 10:46:10, "Justin Lemkul"  wrote:
> >
> >
> >On 7/30/17 8:58 PM, YanhuaOuyang wrote:
> >> Hi,
> >>   I have run a protein MD simulation and choose a force field "8:
> CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder
> that whether the CHARMM27 all-atom force field here is equal to the
> CHARMM22/CMAP
> >>
> >
> >Well, not "equal" but it means that the "CHARMM27" files include C22/CMAP
> for
> >proteins.  There is no such thing as a CHARMM27 protein force field.  The
> C27
> >nucleic acid and lipid parameters came out at the same time as the
> C22/CMAP
> >protein force field, and got somewhat unfortunately lumped together in
> nomenclature.
> >
> >-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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> --
>
> Message: 2
> Date: Mon, 31 Jul 2017 14:19:07 +0900
> From: ? ?   
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] gmx mdmat calculation of heavy atoms of two side
> chains
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx users,
>
> I would like to know about the hydrophobic interaction between heavy atoms
> of side chains in different chains of peptides. How can I use mdmat tool
> for this calculation? I  separately indexed all heavy atoms but mdmat use
> only one index group in the calculation. I re-integrated all separate
> groups into a group. Calculation result came out only two side chain
> distance image.
> If you have any suggestion please help me?
>
>
> Best regards,
> Mijee
>
>
> --
>
> Message: 3
> Date: Mon, 31 Jul 2017 07:29:19 +
> From: "Pandya, Akash" 
> To: "gmx-us...@gromacs.org" 
> Subject: [gmx-users] RDF Values
> Message-ID:
>

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