[gmx-users] importance of nvlink in GPU nodes?

[Christopher Neale]

Dear users:

does anybody know if the presence of either CPU-to-GPU or GPU-to-GPU nvlink 
affects the performance or efficiency of gromacs?

Thank you,
Chris.
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Re: [gmx-users] Replica Exchange for surface tension

[Justin Lemkul]

On 3/28/17 2:59 PM, gozde ergin wrote:

I use Charmm36 force field. Do you mean the force field parameter between
cocobetaine and SDS? Because for pure surfactant I am able to estimate the
correct surface tension. Which means force field parameter of SDS-water and
cocobetaine-water is fine.



SDS is a standard part of CHARMM36 but I have no idea what cocobetaine is.  Did 
you find existing parameters for it or did you do the parametrization yourself? 
The larger point is that you've probably stumbled upon the corner cases that 
often come up - some combination of parameters has never been looked at before 
and it requires more refinement.  If both interact with water fine but interact 
with each other improperly, that means either the SDS-cocobetaine interactions 
are too weak or too strong, or that they induce some sort of abnormal 
conformational sampling.


You'll need to look at the microscopic details of how they interact - which 
groups are associated with which, how the conformational ensembles of each 
differ from those observed in water, etc.  Then you can focus on specific 
elements of refinement that may need to be done (e.g. NBFIX for LJ interactions 
that are often the culprit in such cases, and/or perhaps some sub-par dihedral 
parameters that lead to bad sampling when a particular interaction occurs).


-Justin


Sent from my iPhone


On 28 Mar 2017, at 7:21 PM, Justin Lemkul  wrote:




On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and
cocobetaine on water surface. I estimated the surface tension of SDS on
water surface and cocabetaine on surface tension separately and correctly
(comparing with experimental results). However I could not estimate the
correct surface tension for SDS-cocobetaine mix in even 150 ns
simulation. Do you think replica exchange simulation would help me to
estimate the correct surface tension of mixed system? Do you have any
idea why I failed in estimating the mixed system surface tension?



If a physical model fails to produce known physical properties, the problem
is often the model itself.  I'd suspect the force field parameters first.
What is the source of your parameters?

Replica exchange helps you get over large barriers to improve sampling, but
I doubt that's useful here in a mixture of small molecules.

-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] Replica Exchange for surface tension

[gozde ergin]

I use Charmm36 force field. Do you mean the force field parameter between 
cocobetaine and SDS? Because for pure surfactant I am able to estimate the 
correct surface tension. Which means force field parameter of SDS-water and 
cocobetaine-water is fine.

Sent from my iPhone

> On 28 Mar 2017, at 7:21 PM, Justin Lemkul  wrote:
> 
> 
> 
>> On 3/28/17 12:43 PM, gozde ergin wrote:
>> I have a mixed system of SDS and cocobetaine on water surface.
>> I estimated the surface tension of SDS on water surface and cocabetaine on 
>> surface tension separately and correctly (comparing with experimental 
>> results).
>> However I could not estimate the correct surface tension for SDS-cocobetaine 
>> mix in even 150 ns simulation.
>> Do you think replica exchange simulation would help me to estimate the 
>> correct surface tension of mixed system?
>> Do you have any idea why I failed in estimating the mixed system surface 
>> tension?
>> 
> 
> If a physical model fails to produce known physical properties, the problem 
> is often the model itself.  I'd suspect the force field parameters first.  
> What is the source of your parameters?
> 
> Replica exchange helps you get over large barriers to improve sampling, but I 
> doubt that's useful here in a mixture of small molecules.
> 
> -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] MD for inorganic compound

[André Farias de Moura]

Fixed charges may work as well, although some parameterization might be
necessary.

there are plenty of papers reporting such simulations, for instance:

Langmuir, 2015, 31 (48), pp 13127–13137
*DOI: *10.1021/acs.langmuir.5b03167


On Tue, Mar 28, 2017 at 2:27 PM, Michael Brunsteiner 
wrote:

> > Anjali Patel wrote:> What is the procedure of using gromacs specially
> for inorganic compound??> I am beginner for gromacs simulation package, I
> used it for organic
> > compounds. But unable to understand how to deal with inorganic compounds
> > and what about the force field and solvent we can use.
> as Justin wrote, you can use gromacs to model any material on the
> molecular scaleas long as you have a decent force field.This being said:
> gromacs was originally built primarily with (bio-)organiccompounds in mind,
> and here the fixed partial charge model that is defaultin gromacs is good
> enough in many cases. When you deal with inorganic compoundsespecially with
> salts and/or materials in the solid state accounting for polarizability
> mightbe essential for getting good results. In this case you have two
> choices:
> 1) stick with gromacs and use the shell model. Here its worthwhile looking
> at the   work of Richard Catlow and co-workers. they did a lot of work in
> this field - however,
>   be careful here as published shell-model force fields are in most cases
> not widely tested  compared to the commonly used fixed charge force fields.
>
> 2) turn to DFT/plain wave basis set models and software
>(see https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_
> solid-state_physics_software)
>
> cheers,
> Michael
>
> > With regards
> > Anjali Patel
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_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] Help in a thermalization

[Graziele Bortolini]

It worked.
Thanks Justin.

2017-03-27 18:23 GMT-03:00 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
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
>>
> --
> ==
>
> 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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-- 
Att.
G. Bortolini
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[gmx-users] MD for inorganic compound

[Michael Brunsteiner]

> Anjali Patel wrote:> What is the procedure of using gromacs specially for 
> inorganic compound??> I am beginner for gromacs simulation package, I used it 
> for organic
> compounds. But unable to understand how to deal with inorganic compounds
> and what about the force field and solvent we can use.
as Justin wrote, you can use gromacs to model any material on the molecular 
scaleas long as you have a decent force field.This being said: gromacs was 
originally built primarily with (bio-)organiccompounds in mind, and here the 
fixed partial charge model that is defaultin gromacs is good enough in many 
cases. When you deal with inorganic compoundsespecially with salts and/or 
materials in the solid state accounting for polarizability mightbe essential 
for getting good results. In this case you have two choices:
1) stick with gromacs and use the shell model. Here its worthwhile looking at 
the   work of Richard Catlow and co-workers. they did a lot of work in this 
field - however, 
  be careful here as published shell-model force fields are in most cases not 
widely tested  compared to the commonly used fixed charge force fields.

2) turn to DFT/plain wave basis set models and software 
   (see 
https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software)

cheers,
Michael

> With regards
> Anjali Patel
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Re: [gmx-users] Replica Exchange for surface tension

[Justin Lemkul]

On 3/28/17 12:43 PM, gozde ergin wrote:

I have a mixed system of SDS and cocobetaine on water surface.
I estimated the surface tension of SDS on water surface and cocabetaine on 
surface tension separately and correctly (comparing with experimental results).
However I could not estimate the correct surface tension for SDS-cocobetaine 
mix in even 150 ns simulation.
Do you think replica exchange simulation would help me to estimate the correct 
surface tension of mixed system?
Do you have any idea why I failed in estimating the mixed system surface 
tension?



If a physical model fails to produce known physical properties, the problem is 
often the model itself.  I'd suspect the force field parameters first.  What is 
the source of your parameters?


Replica exchange helps you get over large barriers to improve sampling, but I 
doubt that's useful here in a mixture of small molecules.


-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] About msd and lateral diffussion command

[Justin Lemkul]

On 3/28/17 12:17 PM, Poncho Arvayo Zatarain wrote:



Hello gromacs user: I want to obtain the msd and lateral diffussion for
dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc
-lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2
& 3 are dppc and dppe. Wht do you think about my command? It´s ok or is there
anything wrong?.



What happened when you gave the command?

-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] Replica Exchange for surface tension

[gozde ergin]

I have a mixed system of SDS and cocobetaine on water surface.
I estimated the surface tension of SDS on water surface and cocabetaine on 
surface tension separately and correctly (comparing with experimental results).
However I could not estimate the correct surface tension for SDS-cocobetaine 
mix in even 150 ns simulation.
Do you think replica exchange simulation would help me to estimate the correct 
surface tension of mixed system?
Do you have any idea why I failed in estimating the mixed system surface 
tension?

Thanks in advance.

-- 
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[gmx-users] About msd and lateral diffussion command

[Poncho Arvayo Zatarain]

Hello gromacs user: I want to obtain the msd and lateral diffussion for 
dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc 
-lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2 & 
3 are dppc and dppe. Wht do you think about my command? It´s ok or is there 
anything wrong?.
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Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

[spss4]

 - Message from Mark Abraham  -
    Date: Tue, 28 Mar 2017 12:04:42 +
    From: Mark Abraham 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic
SASA separately in latest version of gromacs?
      To: gmx-us...@gromacs.org


Hi,

Did


http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas

help?

Mark

On Tue, Mar 28, 2017 at 7:31 AM  wrote:


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

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
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- End message from Mark Abraham  -

Hii
Thank you for your help. I have tried this already but I cannot execute
this command properly(getting some errors). Can you send me the exact
command what I have to use to get hydrophobic and hydrophilic sasa
separately?
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Re: [gmx-users] protein-ligand

[RAHUL SURESH]

Yeah. Thank you Mr.Justin

On Tue, Mar 28, 2017 at 7:43 PM, Justin Lemkul  wrote:

>
>
> On 3/28/17 10:06 AM, RAHUL SURESH wrote:
>
>> But in case of charmm36ff, the script file will not generate .gro file for
>> ligand  I believe. In that case how will i generate gro file?
>>
>>
> I responded to your exact same question yesterday.  Please read that.
>
> -Justin
>
>
> On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 3/27/17 11:49 PM, RAHUL SURESH wrote:
>>>
>>> How will I add ligand .gro file in protein .gro file to make a complex .?


>>> With a text editor.  Go through my tutorial:
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/complex/index.html
>>>
>>> -Justin
>>>
>>>
>>> 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
>
> ==
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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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>>> Gromacs Users mailing list
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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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] protein-ligand

[Justin Lemkul]

On 3/28/17 10:06 AM, RAHUL SURESH wrote:

But in case of charmm36ff, the script file will not generate .gro file for
ligand  I believe. In that case how will i generate gro file?



I responded to your exact same question yesterday.  Please read that.

-Justin


On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul  wrote:




On 3/27/17 11:49 PM, RAHUL SURESH wrote:


How will I add ligand .gro file in protein .gro file to make a complex .?



With a text editor.  Go through my tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
-tutorials/complex/index.html

-Justin


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

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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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] protein-ligand

[RAHUL SURESH]

But in case of charmm36ff, the script file will not generate .gro file for
ligand  I believe. In that case how will i generate gro file?

On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul  wrote:

>
>
> On 3/27/17 11:49 PM, RAHUL SURESH wrote:
>
>> How will I add ligand .gro file in protein .gro file to make a complex .?
>>
>
> With a text editor.  Go through my tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
> -tutorials/complex/index.html
>
> -Justin
>
>
> 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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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> 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] Pull Code constant value

[Vytautas Rakeviius]

I suggest trial and error in quite short runs without wasting time on waiting 
for next day or so. Really large k can create segmentation faults or 
"cannonball into wall" like effects in MD movie.
 

On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary 
 wrote:
 

 Hi all,

I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate this
value or it simply based on the trial-and-error method?

Also, what problems can take place if the value is large (huge, I guess)?

Thanks,

Souparno Adhikary
University of Calcutta.
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Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

[Mark Abraham]

Hi,

Avoiding these kind of artefacts is exactly why the recommended procedure
is to follow
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Mark

On Tue, Mar 28, 2017 at 2:02 PM Justin Lemkul  wrote:

>
>
> On 3/28/17 4:26 AM, Erik Marklund wrote:
> > Dear Yvon,
> >
> > Are you sure you ‘re not constraining, say, H-bonds in one and not the
> other?
> >
>
> This is almost certainly the case.  We've done extensive validation of
> CHARMM
> vs. GROMACS energies and the agreement is nearly perfect if calculated
> properly.
>
> -Justin
>
> > Kind regards,
> > Erik
> > __
> > Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> > Department of Chemistry – BMC, Uppsala University
> > +46 (0)18 471 4539 <018-471%2045%2039>
> > erik.markl...@kemi.uu.se
> >
> > On 28 Mar 2017, at 07:55, Yvon Wong > wrote:
> >
> > 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
> > --
> > 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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> send a mail to gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org>.
> >
>
> --
> ==
>
> 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] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

[Mark Abraham]

Hi,

Did
http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas
 help?

Mark

On Tue, Mar 28, 2017 at 7:31 AM  wrote:

>
>
>
> -- Forwarded message --
> From: sp...@iacs.res.in
> To: gmx-us...@gromacs.org
> Cc:
> Bcc:
> Date: Fri, 24 Mar 2017 16:24:21 +0530
> Subject: How to calculate Hydrophobic and Hydrophilic SASA separately in
> latest version of gromacs?
>
> 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
> --
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Re: [gmx-users] dihedral restrains fail in free energy calculation

[Justin Lemkul]

On 3/28/17 6:07 AM, Ahmet Yıldırım wrote:

Dear users,

I was trying to do the free energy calculation on GROMACS-2016.1 but I
faced a problem. To apply intermolecular restraints I add the [
intermolecular_interactions ] part at the end of complex topology file.
First I turn off intermolecular interactions and then turn them on one by
one. Intermolecular bond and angle restraints work together, but dihedral
restraints fail when decoupling the ligand. That means every three
restraints (bond, angle and dihedral) don't work together when ligand is
decoupled from protein. The system gives lincs warning error in the NVT,
NPT or md step for different ligands. The same systems work properly for
the ligand bound state with the same intermolecular interactions. Could
someone give me some pointers about
why the dihedral restraints fail when decoupling the ligand?

Some more details on simulation: I use sd integrator, AMBER99-ILDN
force-field, tip3p water model, constraint on Hydrogen atoms, position
restraint at NVT and NPT.

The ID of atoms used for intermolecular_interactions are as follows. The
backbone atoms of aminoacid that is the closest one to the ligand:
1793: C of the carboxyl group of amino acid
1778: C_alpha atom of amino acid
1776: N of amino acid

The ID of heavy atoms of ligand:
3: O2
2: O1
1: S1

Free energy control stuff used in the mdp files of the decoupled state is
here:
free-energy  = yes
init-lambda  = 1
delta-lambda = 0
sc-alpha = 0.3
sc-power = 1
sc-sigma = 0.25
sc-coul  = yes
couple-moltype   = ligand
couple-intramol  = no
couple-lambda0   = vdw-q
couple-lambda1   = none
nstdhdl  = 100

[ intermolecular_interactions ] part in the complex topology identifies a
suitable set of Boresch restraints. The last part of the complex.top is as
follows:

[ molecules ]
; Compound#mols
ligand   1
protein 1
SOL 4812
NA 30
CL 15

[ intermolecular_interactions ]
[ bonds ]
;i j  type r0A r1A r2AfcAr0B r1B r2B
fcB
 1776 2 10 0.3198 0.319810.  0.000 0.3198
0.319810.   4184.000

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
multB
 1778  1776 2  1776  1   132.7383  0.000  1
132.7383 41.840  1
 1776 2 1 2  1   157.5476  0.000  1
157.5476 41.840  1

[ dihedral_restraints ]
;   aiajakal  typephiA dphiA  fcAphiB  dphiB
fcB
 1793  1778  1776 2  165.9452 0.  0.000
65.9452 0. 41.840
 1778  1776 2 1  198.2017 0.  0.000
98.2017 0. 41.840
 1776 2 1 3  1   179.1898 0.  0.000
179.1898 0. 41.840



It's really easy to choose "bad" atoms for restraining.  Consider the points in 
dx.doi.org/10.1021/ci300505n, and cited work by Boresch, Roux, etc. in 
determining the proper restraints.  I have found that virtual sites constructed 
in the middle of rings are very effective in accomplishing orientational 
restraints, even in very complex systems.  They run without a hitch if chosen 
judiciously.


-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] MD for inorganic compound

[Justin Lemkul]

On 3/28/17 5:00 AM, Anjali Patel wrote:

What is the procedure of using gromacs specially for inorganic compound??

I am beginner for gromacs simulation package, I used it for organic
compounds. But unable to understand how to deal with inorganic compounds
and what about the force field and solvent we can use.



There's nothing really special here except to make sure you have a proper force 
field that can adequately model whatever species you care about.  You won't find 
that likely built in to GROMACS already, but in concert with what you find in 
the literature and Chapter 5 of the GROMACS manual, surely you can build a force 
field that suits your needs.  GROMACS can do whatever you tell it to do :)


-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] topology

[Justin Lemkul]

On 3/27/17 11:51 PM, RAHUL SURESH wrote:

So it is mandatory to add


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


In top file.?



You can't simulate a drug molecule without telling grompp what it's parameters 
are so that mdrun can simulate it.


-Justin



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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--
==

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 11:49 PM, RAHUL SURESH wrote:

How will I add ligand .gro file in protein .gro file to make a complex .?


With a text editor.  Go through my tutorial: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html


-Justin


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

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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

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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] Bond energy difference between CHARMM and GROMACS

[Justin Lemkul]

On 3/28/17 4:26 AM, Erik Marklund wrote:

Dear Yvon,

Are you sure you ‘re not constraining, say, H-bonds in one and not the other?



This is almost certainly the case.  We've done extensive validation of CHARMM 
vs. GROMACS energies and the agreement is nearly perfect if calculated properly.


-Justin


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

On 28 Mar 2017, at 07:55, Yvon Wong 
> wrote:

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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School of Pharmacy
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University of Maryland, Baltimore
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Re: [gmx-users] forcefield installation on GROMACS 5.1.4

[Justin Lemkul]

On 3/28/17 3:12 AM, Simon Kit Sang Chu wrote:

Dear Justin,

Thank you very much. I followed the same spirit and add forcefield.doc.
However, it did not work until changing all ffPACE_1.5.rtp .ddb .etc
files into aminoacids.rpt .ddb . GROMACS seems to recognize only the
name "aminoacids". Also, don't forget to change the ffPACE1.5.itp to
*forcefield.itp* instead of aminoacids.itp.



That's not strictly true; the .rtp files can be named anything.  I don't know 
why you encountered problems, but many force fields use different names.  The 
naming scheme may require a match in base name between an .rtp and an .hdb file, 
but there is flexibility (for instance, we use "merged.rtp" in our CHARMM36 port 
because it's a lot of stuff in one file, not just protein residues).


-Justin


Regards,
Simon

2017-03-28 0:54 GMT+08:00 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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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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 11:34 PM, Dilip H N wrote:

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...??



By making two groups instead of one.  That's what an RDF tells you - how the 
atoms in group X are distributed around the atoms in group Y.  The typo is 
insignificant because now we're just talking about N-terminal protons instead of 
alpha H atoms.  My previous points stand.


-Justin





   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


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 

[gmx-users] Pull Code constant value

[Souparno Adhikary]

Hi all,

I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate this
value or it simply based on the trial-and-error method?

Also, what problems can take place if the value is large (huge, I guess)?

Thanks,

Souparno Adhikary
University of Calcutta.
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[gmx-users] rotation while pulling

[gromacs query]

Hi All,

{apologies if posted multiple times; seems like some trouble with my
account}

I want to pull linear molecule across the membrane in two ways allowing:
- translation along Z and rotation around Z
- translation along Z and rotation in all axes

My current mdp-setting pulls molecular along Z but it translates and
rotates in all axes. Do I need to use some advanced options?

; Pull Code
pull= umbrella
pull_geometry   = direction
pull-vec1 = 0 0 -1
pull_dim= N N Y ;
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = MEM ; restrained group
pull_group1 = LIG; group to pull
pull_init1 = 0
pull_rate1  = 0.1; nm per ps
pull_k1 = 1000   ; kJ mol^-1 nm^-2


Also in this case would it be wise to use/say absolute Z coordinate as
reaction coordinate? rather center of mass distances between membrane and
ligand.

Thanks
Jiom
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[gmx-users] dihedral restrains fail in free energy calculation

[Ahmet Yıldırım]

Dear users,

I was trying to do the free energy calculation on GROMACS-2016.1 but I
faced a problem. To apply intermolecular restraints I add the [
intermolecular_interactions ] part at the end of complex topology file.
First I turn off intermolecular interactions and then turn them on one by
one. Intermolecular bond and angle restraints work together, but dihedral
restraints fail when decoupling the ligand. That means every three
restraints (bond, angle and dihedral) don't work together when ligand is
decoupled from protein. The system gives lincs warning error in the NVT,
NPT or md step for different ligands. The same systems work properly for
the ligand bound state with the same intermolecular interactions. Could
someone give me some pointers about
why the dihedral restraints fail when decoupling the ligand?

Some more details on simulation: I use sd integrator, AMBER99-ILDN
force-field, tip3p water model, constraint on Hydrogen atoms, position
restraint at NVT and NPT.

The ID of atoms used for intermolecular_interactions are as follows. The
backbone atoms of aminoacid that is the closest one to the ligand:
1793: C of the carboxyl group of amino acid
1778: C_alpha atom of amino acid
1776: N of amino acid

The ID of heavy atoms of ligand:
3: O2
2: O1
1: S1

Free energy control stuff used in the mdp files of the decoupled state is
here:
free-energy  = yes
init-lambda  = 1
delta-lambda = 0
sc-alpha = 0.3
sc-power = 1
sc-sigma = 0.25
sc-coul  = yes
couple-moltype   = ligand
couple-intramol  = no
couple-lambda0   = vdw-q
couple-lambda1   = none
nstdhdl  = 100

[ intermolecular_interactions ] part in the complex topology identifies a
suitable set of Boresch restraints. The last part of the complex.top is as
follows:

[ molecules ]
; Compound#mols
ligand   1
protein 1
SOL 4812
NA 30
CL 15

[ intermolecular_interactions ]
[ bonds ]
;i j  type r0A r1A r2AfcAr0B r1B r2B
fcB
 1776 2 10 0.3198 0.319810.  0.000 0.3198
0.319810.   4184.000

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
multB
 1778  1776 2  1776  1   132.7383  0.000  1
132.7383 41.840  1
 1776 2 1 2  1   157.5476  0.000  1
157.5476 41.840  1

[ dihedral_restraints ]
;   aiajakal  typephiA dphiA  fcAphiB  dphiB
fcB
 1793  1778  1776 2  165.9452 0.  0.000
65.9452 0. 41.840
 1778  1776 2 1  198.2017 0.  0.000
98.2017 0. 41.840
 1776 2 1 3  1   179.1898 0.  0.000
179.1898 0. 41.840

Cheers,

-- 
Ahmet Yıldırım
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Re: [gmx-users] solvate with hexagonal box

[Erik Marklund]

Done! https://redmine.gromacs.org/issues/2148

On 28 Mar 2017, at 10:24, Erik Marklund 
> wrote:

Hi Mark,

Thanks. I will do so once my collaborators confirm that it’s ok that I upload 
the structure files.

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

On 27 Mar 2017, at 20:20, Mark Abraham 
>
 wrote:

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

[Michael Brunsteiner]

Thanks Peter and Mark!
I'll try running on single cores ...
however, comparing the timings I believe the bottleneck might be the time spent 
in I/O(reading/writing to disk) and here running several jobs on a single node 
with multiple coresmight make things even worse.
also funny: In the log files Gromacs reports Wall times for both machines that 
are comparable:0.613 (old machine)0.525 (new machine)but the UNIX time command 
tells a different story:
real    0m0.798s (old machine)
real    0m1.543s (new machine)
i wonder where the missing time goes ... ;)

anyway thanks again!regardsMichael
 === Why be happy when you could be normal?
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[gmx-users] MD for inorganic compound

[Anjali Patel]

What is the procedure of using gromacs specially for inorganic compound??

I am beginner for gromacs simulation package, I used it for organic
compounds. But unable to understand how to deal with inorganic compounds
and what about the force field and solvent we can use.


With regards
Anjali Patel
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Re: [gmx-users] Align a vector with an axis of the box

[Chalaoux, Francois-Regis]

Hi All and thank you Mark for your answer,

I created a vector with make_ndx between 2 atoms but I can't find how to use 
this vector with the editconf command. The "rotate" option needs for a vector 
representing the rotation around axis Z ( 0 , 0 , 60) but the result seems not 
to be of this amplitude. At startup, the choice with editconf seems not to give 
the possibility to choose my vector, only the system size (I chose my vector) 
and the group for output (I chose system).

gmx editconf -f complex.gro -o newbow.gro -bt cubic -n index_vect1.ndx -d 1.0 
-rotate 0 0 60

Any idea ?

FR.

-Message d'origine-
De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Mark 
Abraham
Envoyé : jeudi 23 mars 2017 15:37
À : gmx-us...@gromacs.org
Objet : Re: [gmx-users] Align a vector with an axis of the box

Hi,

I can't comment on the appropriateness of your protocol, but to implement it, 
take your solute and use editconf to rotate it so your intended vector so it 
aligns with an appropriate axis, and put e.g. a suitable rectilinear box on 
that before filling it with solvent.

Mark

On Thu, Mar 23, 2017 at 3:25 PM Chalaoux, Francois-Regis < 
francois-regis.chala...@evotec.com> wrote:

> Hi All,
>
> To realize an umbrella sampling of JZ4 in the Lyzosyme (3HTB) I have 
> to define a box enough long to pull JZ4. I choose a reaction 
> coordinate between Calpha THR109 and JZ4-COM.
> Presently, this coordinate (vector) is not aligned with an axis of my 
> cubic box and after a pulling should exceed the one-half of the final 
> box and create an interaction with an image with PBC. So I would like 
> to align this vector with an axis of the box. If my protocol makes 
> sens , How to align this vector with an axis of the box ?
>
>
> Cheers, FR.
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Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

[Erik Marklund]

Dear Yvon,

Are you sure you ‘re not constraining, say, H-bonds in one and not the other?

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

On 28 Mar 2017, at 07:55, Yvon Wong 
> wrote:

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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Re: [gmx-users] solvate with hexagonal box

[Erik Marklund]

Hi Mark,

Thanks. I will do so once my collaborators confirm that it’s ok that I upload 
the structure files.

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

On 27 Mar 2017, at 20:20, Mark Abraham 
> wrote:

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] forcefield installation on GROMACS 5.1.4

[Simon Kit Sang Chu]

Dear Justin,

Thank you very much. I followed the same spirit and add forcefield.doc.
However, it did not work until changing all ffPACE_1.5.rtp .ddb .etc
files into aminoacids.rpt .ddb . GROMACS seems to recognize only the
name "aminoacids". Also, don't forget to change the ffPACE1.5.itp to
*forcefield.itp* instead of aminoacids.itp.

Regards,
Simon

2017-03-28 0:54 GMT+08:00 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] Bond energy difference between CHARMM and GROMACS

[David van der Spoel]

The correct value for kcal conversion is 4.184, however that does not 
explain the difference. Maybe you can try to take one exampel, e.g. the 
first one and test it bond by bond (by turning on one term at a time in 
the topology). I assume this is for 0 steps of MD or EM?



Den 2017-03-28 kl. 07:55, skrev 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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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se

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