Re: [gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

[Nikhil Maroli]

Hi,
i have included the restrain file,the whole MD system is obtained from 
charmm-gui ,and i have included restrain too

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Re: [gmx-users] gmx convert-tpr, gmx check Q ?

[Justin Lemkul]

On 4/12/16 9:24 AM, badamkhatan togoldor wrote:

Thank you for reply of Justin. So as I understood from there no need to 
convert-tpr and just do it like,
  gmx mdrun -deffnm pro$ -cpi pro1.cpt  -append
That's it ?



Yes.

-Justin



   From: Justin Lemkul 
  To: gmx-us...@gromacs.org
  Sent: Tuesday, 12 April 2016, 15:23
  Subject: Re: [gmx-users] gmx convert-tpr, gmx check Q ?



On 4/12/16 8:16 AM, badamkhatan togoldor wrote:

Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr
and gmx check.  I have a little bit doubt in that.  Simulation was
calculating 5.000.000 steps, 10ns and it has stopped due to the some cluster
time limit. So I want to continue it from that stopped step. So, gmx
convert-tpr -s pro.tpr -f pro.trr -e pro.edr -o pro1.tpr -until 1 ( it


There is no need to invoke convert-tpr for a run that stopped prematurely.


means that when checked the gmx check the .tpr file it says 4688 step and 1
ps. From this step until finish to 10 ps?)And also 10,000 ps  is 10 ns
right? then why gmx check gave me the 1 ps ? or is it 1 ns ?


The timestep here (in ps, as noted) is the interval between frames.


Item#frames Timestep (ps)

  > Step  46881
  > Time  46881
  > Lambda46881

Coords46881

gmx mdrun -deffnm $pro -append -cpi which check point file I should apply
pro.cpt  OR pro_prev.cpt ? I would highly appreciate for any answers! Thanks



What does gmx check tell you about the contents of each of these?  The help info
for mdrun also explains the checkpointing mechanism and the difference in these
files, so start by reading that.

-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] Question for Gromacs Users

[Justin Lemkul]

On 4/12/16 2:22 PM, Brier, Troy wrote:

To whom it may concern,

I am attempting to run a single protein in water Martini coarse grain
simulation. I used martinize.py (version 2.4) to coarse grain the
protein and add a dilsulfide bond. When attempting to run the
minimization phase (I am using Gromacs version 5.1) I receive the
following error:

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For
more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors

After troubleshooting I determined the error came from the Bonds
section in the Protein_A.itp file produced from martinize.py, and
specifically from the section having to do with the disulfide bonds.
The error seems to be related to martinize.py determining the bond
constraints of the disulfide bone to not match those of the literature
values, and the script prints the following message:

Note: Cysteine bonds are 0.24 nm constraints, instead of the published
0.39nm/5000kJ/mol.

So I changed the section in the Protein_A.itp file from:

(Error Causing  Protein_A.itp file under [bonds])
; Links/Cystine bridges
   253   281  1   0.24000

to:

  (Error Causing  Protein_A.itp file under [bonds])
; Links/Cystine bridges
   253   281  1   0.39000 5000


and then the minimization step runs without the fatal error. What I
would like to know if making this change is the proper thing to do or
should I keep the constraint distance at 0.24 nm and just add in the
bond strength of 5000 kJ/mol?



The wording of the error message states that it's supposed to be a constraint 
(i.e. fixed distance), not a harmonic interaction.  So if it's a constraint, 
it's simply being written to the wrong section of the topology.  It may be 
better to post this question to the MARTINI forum.  A difference between a rigid 
0.24 nm distance and a harmonic 0.39 nm distance is quite substantial.


-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] Question for Gromacs Users

[Brier, Troy]

To whom it may concern,

I am attempting to run a single protein in water Martini coarse grain
simulation. I used martinize.py (version 2.4) to coarse grain the
protein and add a dilsulfide bond. When attempting to run the
minimization phase (I am using Gromacs version 5.1) I receive the
following error:

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For
more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors

After troubleshooting I determined the error came from the Bonds
section in the Protein_A.itp file produced from martinize.py, and
specifically from the section having to do with the disulfide bonds.
The error seems to be related to martinize.py determining the bond
constraints of the disulfide bone to not match those of the literature
values, and the script prints the following message:

Note: Cysteine bonds are 0.24 nm constraints, instead of the published
0.39nm/5000kJ/mol.

So I changed the section in the Protein_A.itp file from:

(Error Causing  Protein_A.itp file under [bonds])
; Links/Cystine bridges
  253   281  1   0.24000

to:

 (Error Causing  Protein_A.itp file under [bonds])
; Links/Cystine bridges
  253   281  1   0.39000 5000


and then the minimization step runs without the fatal error. What I
would like to know if making this change is the proper thing to do or
should I keep the constraint distance at 0.24 nm and just add in the
bond strength of 5000 kJ/mol?

Thanks for your help,

Troy Brier
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Re: [gmx-users] Preparing dual topology for free energy calculation

[Dries Van Rompaey]

Hi,

You should contact the tool's authors for that issue. I don't have any
experience with it.

Good luck

Dries
Hi Rompaey,
Thanks for your valuable advice. As per your advice I went through the
paper (
https://www.google.be/url?sa=t=web=j=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872215/=0ahUKEwjq3I7M-YbMAhXI_w4KHQeeCX8QFggoMAU=AFQjCNHnkqQys4V7UYCURTPZyKQEYrGdWQ=rpmfKD8E07TCQ_XfeUyE3Q
).


They also used dual topology approach. They use pmx to generate those
topology. Unfortunately the same program didn't work for me. It gives the
following error (mentioned at the bottom) which I couldn't solve. I went
through many tutorial and on line material but everywhere people talk about
binding energy with ligand. Also they provide topology file and don't
describe how to generate one. I will be grateful if I can get some other
option to prepare dual topology or calculate free energy without dual
topology.

Error message from pmx:

Traceback (most recent call last):
  File "/home/madhu/pmx/scripts/mutate.py", line 504, in 
main(sys.argv)
  File "/home/madhu/pmx/scripts/mutate.py", line 495, in main
apply_mutation( m, mutation, mtp_file )
  File "/home/madhu/pmx/scripts/mutate.py", line 354, in apply_mutation
apply_aa_mutation(m, residue, new_aa_name, mtp_file)
  File "/home/madhu/pmx/scripts/mutate.py", line 332, in apply_aa_mutation
bb_super(residue, hybrid_res )
  File "/usr/local/lib/python2.7/dist-packages/pmx/geometry.py", line 168,
in bb_super
assert len(atoms1) == len(atoms2), "%s -> %s" % ( '-'.join( map(lambda
a: a.name, atoms1)),'-'.join( map(lambda a: a.name, atoms2)) )

Thanks a lot.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

[Christopher Neale]

This is not enough detail for us to know what the problem is. Did you set 
things up correctly so that posre_cpn.itp is actually used? You can check by 
gmx energy and see if you have restraint energies there. To use these 
restraints your .top file needs to #include "posre_cpn.itp" , which you can do 
directly or via an #ifdef statement in the cpn.itp topology and 
define=-DSOME_IDENTIFIER in your .mdp file  you can see how this is done in 
your .top file for water.

Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nikhil Maroli 

Sent: 12 April 2016 09:25
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] wanted to fix cpn in lipid layer MD,   
-position/distance restrains

Dear all,
i am doing MD of cyclic peptide nanotube in lipids,i wanted to keep the
tube fixed thoughout simulation but with below restrains after 40ns two to
three rings moves away from the positions .

gmx genrestr -f cpn.gro -o posre_cpn.itp -fc 1000 1000 1000


i wanted to  keep the position  fixed or maximum +1 nm movements of
individual rings , so can anyone suggest

me how should i proceed  i dont have time to check all the possibility
of gmx genrestr

so specifically hwo should i procees in such cases

Thanks



--
Ragards,
Nikhil Maroli
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Re: [gmx-users] Details of 5.0 benchmark report?

[Szilárd Páll]

Adam,

The job scripts used in those benchmarks are all specific to the
machines, and while admittedly the launch configuration information
could be useful to have next to each data point, I'm afraid we don't
have such data readily extracted from the run logs, I believe. I did
not compile the document myself, but unless such data has been parsed
and it's just not presented, it would be a quite large effort to go
back and extract such information for quite little benefit (as the
exact ranks/thread configurations will change with GROMACS versions,
compilers, libraries, machine load, etc.)

I recommend you to have a look at recent benchmark papers that contain
detailed information on what to tune and how to run parallel jobs,
e.g.
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full
Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.

Cheers,
--
Szilárd


On Mon, Apr 11, 2016 at 2:00 PM, Adam Huffman  wrote:
> Hello
>
> Ideal would be to have the command-lines that were used, for those of
> us that aren't GROMACS experts.
>
> Cheers,
> Adam
>
> On Tue, Mar 8, 2016 at 5:08 PM, Szilárd Páll  wrote:
>> Hi,
>>
>> What details are you interested in? IIRC the inputs are clearly specified
>> (although perhaps not provided there).
>>
>> --
>> Szilárd
>>
>> On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman  wrote:
>>
>>> Hello
>>>
>>> Are details of the running of the benchmarks reported for version 5.0
>>> available anywhere?
>>>
>>> I'm referring to the report published at:
>>>
>>> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf
>>>
>>> I would like to be able to run these myself, on three different systems.
>>>
>>>
>>> Cheers,
>>> Adam
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>>> posting!
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>>>
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[gmx-users] Run mdrun in parallel

[Husen R]

Hi all,

Currently, I'm trying to run mdrun command in parallel.
the following is my batch script using Slurm as a resource manager:

=Batch Script==
#!/bin/bash
#SBATCH -J Eq1
#SBATCH -o eq1-%j.out
#SBATCH -A pro
#SBATCH -N 2
#SBATCH -n 16

gmx mdrun -deffnm tpr
===End Batch Script===

As we can see from the batch script above, I tried to run mdrun with 2
Nodes and 16 processors.
After the batch job is submitted, I tried to see running process in the
background in each node using htop command and I found that only one node
that run 'gmx mdrun -deffnm tpr' command, there was no running process
called 'gmx mdrun -deffnm tpr' in the other one.

Please, anyone tell me how to run mdrun (or gromacs in general) in parallel
?

note : If I run mpi application, I always able to see it running in every
allocated nodes using htop.

thank you in advance.

Regards,


Husen
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Re: [gmx-users] gmx convert-tpr, gmx check Q ?

[badamkhatan togoldor]

Thank you for reply of Justin. So as I understood from there no need to 
convert-tpr and just do it like,
 gmx mdrun -deffnm pro$ -cpi pro1.cpt  -append 
That's it ?


  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Tuesday, 12 April 2016, 15:23
 Subject: Re: [gmx-users] gmx convert-tpr, gmx check Q ?
   


On 4/12/16 8:16 AM, badamkhatan togoldor wrote:
> Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr
> and gmx check.  I have a little bit doubt in that.  Simulation was
> calculating 5.000.000 steps, 10ns and it has stopped due to the some cluster
> time limit. So I want to continue it from that stopped step. So, gmx
> convert-tpr -s pro.tpr -f pro.trr -e pro.edr -o pro1.tpr -until 1 ( it

There is no need to invoke convert-tpr for a run that stopped prematurely.

> means that when checked the gmx check the .tpr file it says 4688 step and 1
> ps. From this step until finish to 10 ps?)    And also 10,000 ps  is 10 ns
> right? then why gmx check gave me the 1 ps ? or is it 1 ns ?

The timestep here (in ps, as noted) is the interval between frames.

> Item        #frames Timestep (ps)
 > Step          4688    1
 > Time          4688    1
 > Lambda        4688    1
> Coords        4688    1
>
> gmx mdrun -deffnm $pro -append -cpi which check point file I should apply
> pro.cpt  OR pro_prev.cpt ? I would highly appreciate for any answers! Thanks
>

What does gmx check tell you about the contents of each of these?  The help 
info 
for mdrun also explains the checkpointing mechanism and the difference in these 
files, so start by reading that.

-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] wanted to fix cpn in lipid layer MD, -position/distance restrains

[Nikhil Maroli]

Dear all,
i am doing MD of cyclic peptide nanotube in lipids,i wanted to keep the
tube fixed thoughout simulation but with below restrains after 40ns two to
three rings moves away from the positions .

gmx genrestr -f cpn.gro -o posre_cpn.itp -fc 1000 1000 1000


i wanted to  keep the position  fixed or maximum +1 nm movements of
individual rings , so can anyone suggest

me how should i proceed  i dont have time to check all the possibility
of gmx genrestr

so specifically hwo should i procees in such cases

Thanks



-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] Preparing dual topology for free energy calculation

[Tushar Ranjan Moharana]

Hi Rompaey,
Thanks for your valuable advice. As per your advice I went through the
paper (
https://www.google.be/url?sa=t=web=j=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872215/=0ahUKEwjq3I7M-YbMAhXI_w4KHQeeCX8QFggoMAU=AFQjCNHnkqQys4V7UYCURTPZyKQEYrGdWQ=rpmfKD8E07TCQ_XfeUyE3Q).


They also used dual topology approach. They use pmx to generate those
topology. Unfortunately the same program didn't work for me. It gives the
following error (mentioned at the bottom) which I couldn't solve. I went
through many tutorial and on line material but everywhere people talk about
binding energy with ligand. Also they provide topology file and don't
describe how to generate one. I will be grateful if I can get some other
option to prepare dual topology or calculate free energy without dual
topology.

Error message from pmx:

Traceback (most recent call last):
  File "/home/madhu/pmx/scripts/mutate.py", line 504, in 
main(sys.argv)
  File "/home/madhu/pmx/scripts/mutate.py", line 495, in main
apply_mutation( m, mutation, mtp_file )
  File "/home/madhu/pmx/scripts/mutate.py", line 354, in apply_mutation
apply_aa_mutation(m, residue, new_aa_name, mtp_file)
  File "/home/madhu/pmx/scripts/mutate.py", line 332, in apply_aa_mutation
bb_super(residue, hybrid_res )
  File "/usr/local/lib/python2.7/dist-packages/pmx/geometry.py", line 168,
in bb_super
assert len(atoms1) == len(atoms2), "%s -> %s" % ( '-'.join( map(lambda
a: a.name, atoms1)),'-'.join( map(lambda a: a.name, atoms2)) )

Thanks a lot.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Justin Lemkul]

On 4/11/16 4:08 PM, Rakesh Sharan wrote:

Hi all,

I am getting significantly different final energy during energy


How large is the difference?  If it is dramatic, then your coordinates should 
also be quite different and visualization should provide some clues.  But given 
that the water molecules are rigid, the only differences will be in nonbonded 
terms, which means a different configuration.  There's no guarantee that two 
constraint algorithms will produce identical outcomes, though I would expect 
them to be close if set up properly.



minimization of a box of bulk TIP4P/2005 water using SETTLE and LINCS as
constraint algorithms. I do not know which is more reliable in the sense
that which one is giving correct converged configurations starting from the
same initial configuration.

I would highly appreciate your comments/suggestions over this discrepancy.

The mdp file that I am using is following:



The .mdp file is not particularly relevant, as using LINCS vs. SETTLE will have 
to be done with changes to the topology file.  If you're getting big differences 
in outcomes, probably whatever modifications you did there are incorrect.


-Justin


integrator  = steep ; steepest descents energy
minimization
nsteps  = 1  ; maximum number of steps to
integrate

emtol   = 1.0  ; [kJ/mol/nm] minimization is
converged when max force is < emtol
emstep  = 0.01  ; [nm] initial step-size

nstxtcout   = 10; [steps] freq to write to
coordinate file
nstlog  = 10; [steps] freq to write energies to
log file
nstenergy   = 10; [steps] freq to write energies to
energy file
xtc_grps= System; coordinate group(s) to write to
disk
energygrps  = System; group(s) to write to energy file

nstlist = 1 ; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions
rlist   = 0.95   ; [nm] cut-off distance for the
short-range neighbor list

rcoulomb= 0.95  ; [nm] distance for Coulomb cut-off

vdw-type= cut-off   ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw= 0.95  ; [nm] distance for LJ cut-off
DispCorr= Ener  ; apply long range dispersion
corrections for energy

;constraints= none
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
fourierspacing  = 0.12

Thanks,

Best.
Rakesh


Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544 (US).



--
==

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 convert-tpr, gmx check Q ?

[Justin Lemkul]

On 4/12/16 8:16 AM, badamkhatan togoldor wrote:

Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr
and gmx check.  I have a little bit doubt in that.  Simulation was
calculating 5.000.000 steps, 10ns and it has stopped due to the some cluster
time limit. So I want to continue it from that stopped step. So, gmx
convert-tpr -s pro.tpr -f pro.trr -e pro.edr -o pro1.tpr -until 1 ( it


There is no need to invoke convert-tpr for a run that stopped prematurely.


means that when checked the gmx check the .tpr file it says 4688 step and 1
ps. From this step until finish to 10 ps?) And also 10,000 ps  is 10 ns
right? then why gmx check gave me the 1 ps ? or is it 1 ns ?


The timestep here (in ps, as noted) is the interval between frames.


Item#frames Timestep (ps)

> Step  46881
> Time  46881
> Lambda46881

Coords46881

gmx mdrun -deffnm $pro -append -cpi which check point file I should apply
pro.cpt  OR pro_prev.cpt ? I would highly appreciate for any answers! Thanks



What does gmx check tell you about the contents of each of these?  The help info 
for mdrun also explains the checkpointing mechanism and the difference in these 
files, so start by reading that.


-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] gmx convert-tpr, gmx check Q ?

[badamkhatan togoldor]

Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr and 
gmx check.  I have a little bit doubt in that.  Simulation was calculating 
5.000.000 steps, 10ns and it has stopped due to the some cluster time limit. So 
I want to continue it from that stopped step. So,
gmx convert-tpr -s pro.tpr -f pro.trr -e pro.edr -o pro1.tpr -until 1 ( it 
means that when checked the gmx check the .tpr file it says 4688 step and 1 ps. 
From this step until finish to 10 ps?)     And also 10,000 ps  is 10 ns right? 
then why gmx check gave me the 1 ps ? or is it 1 ns ?  
 Item    #frames Timestep (ps)
Step  4688    1
Time  4688    1
Lambda  4688    1
Coords   4688    1

gmx mdrun -deffnm $pro -append -cpi which check point file I should apply 
pro.cpt  OR pro_prev.cpt ? 
I would highly appreciate for any answers! Thanks 

Regards,Khatnaa 
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Re: [gmx-users] Gromacs Installation

[ABANTIKA PAL]

Thanks.

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, April 12, 2016 4:54:19 PM
Subject: Re: [gmx-users] Gromacs Installation



On 4/12/16 7:08 AM, ABANTIKA PAL wrote:
> Hi,
>
> I have installed GROMACS 5.1.2 by performing the steps described in the 
> installation guide. All the steps have been executed successfully. But, no 
> executable of mdrun is  created in the build folder. Moreover, upon executing 
> "which gromacs", its showing
>   no gromacs in 
> (/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
> Please help how to resolve the issue.
>

The binary is called gmx.

-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] CHARMM36 ff with NBFIX in grimaces

[gozde ergin]

Thanks Justin.

In order to validate the results from Luo and Roux 2010 study, I need to run 
the simulations with and without NBFIX.
But thank you very much for your respond, I appreciate it.


> On 12 Apr 2016, at 13:25, Justin Lemkul  wrote:
> 
> 
> 
> On 4/12/16 5:35 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I try to simulate the salt solution by using charmm36 ff in gromacs.
>> I downloaded charmm36.ff from MacKerell web page.
>> 
>> 
>> forcefield.to file ;
>> 
>> ; This force field generated by charmm2gmx.py from
>> ; multiple charmm parameter files
>> ; and multiple charmm topology files
>> #define _FF_CHARMM
>> 
>> ; This gromacs version created from:
>> ; CHARMM parameters: multiple files
>> ; CHARMM topology: multiple files
>> [ defaults ]
>> ; nbfunc comb-rule   gen-pairs   fudgeLJ fudgeQQ
>> 12   yes 1.0 1.0
>> 
>> #include "ffnonbonded.itp"
>> #include "ffbonded.itp"
>> #include "gb.itp"
>> #include "cmap.itp"
>> #include “nbfix.itp"
>> 
>> So the last line is nbfix.itp so I assume this force filed comes with 
>> non-bonded fix parameter.
>> But if I want to simulate without NBFIX parameter should I remove this line?
>> 
> 
> You can, but I don't know why you'd want to.  The NBFIXes are considered 
> integral parts of the force field.  If you take them out, you'll risk 
> spurious ion pairing, incorrect osmotic pressure and diffusion, etc. not to 
> mention incorrect interactions among some biomolecules.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
>  before posting!
> 
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> 
> 
> * For (un)subscribe requests visit
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>  or send 
> a mail to gmx-users-requ...@gromacs.org 
> .

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Re: [gmx-users] CHARMM36 ff with NBFIX in grimaces

[Justin Lemkul]

On 4/12/16 5:35 AM, gozde ergin wrote:

Dear all,

I try to simulate the salt solution by using charmm36 ff in gromacs.
I downloaded charmm36.ff from MacKerell web page.


forcefield.to file ;

; This force field generated by charmm2gmx.py from
; multiple charmm parameter files
; and multiple charmm topology files
#define _FF_CHARMM

; This gromacs version created from:
; CHARMM parameters: multiple files
; CHARMM topology: multiple files
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
#include “nbfix.itp"

So the last line is nbfix.itp so I assume this force filed comes with 
non-bonded fix parameter.
But if I want to simulate without NBFIX parameter should I remove this line?



You can, but I don't know why you'd want to.  The NBFIXes are considered 
integral parts of the force field.  If you take them out, you'll risk spurious 
ion pairing, incorrect osmotic pressure and diffusion, etc. not to mention 
incorrect interactions among some biomolecules.


-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 Installation

[Justin Lemkul]

On 4/12/16 7:08 AM, ABANTIKA PAL wrote:

Hi,

I have installed GROMACS 5.1.2 by performing the steps described in the installation 
guide. All the steps have been executed successfully. But, no executable of mdrun is  
created in the build folder. Moreover, upon executing "which gromacs", its 
showing
  no gromacs in 
(/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
Please help how to resolve the issue.



The binary is called gmx.

-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] Gromacs Installation

[ABANTIKA PAL]

Hi,

I have installed GROMACS 5.1.2 by performing the steps described in the 
installation guide. All the steps have been executed successfully. But, no 
executable of mdrun is  created in the build folder. Moreover, upon executing 
"which gromacs", its showing 
 no gromacs in 
(/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
Please help how to resolve the issue.

Thanks and regards

Abantika
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[gmx-users] CHARMM36 ff with NBFIX in grimaces

[gozde ergin]

Dear all,

I try to simulate the salt solution by using charmm36 ff in gromacs.
I downloaded charmm36.ff from MacKerell web page. 


forcefield.to file ;

; This force field generated by charmm2gmx.py from
; multiple charmm parameter files 
; and multiple charmm topology files
#define _FF_CHARMM

; This gromacs version created from:
; CHARMM parameters: multiple files
; CHARMM topology: multiple files
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
#include “nbfix.itp"

So the last line is nbfix.itp so I assume this force filed comes with 
non-bonded fix parameter. 
But if I want to simulate without NBFIX parameter should I remove this line?

Thanks

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[gmx-users] Vizualization of the multi chain protein in MARTINI

[James Starlight]

Dear Gromacs users!

I will be thankfull for any suggestions regarding possibilities of the
discrimination between different chains (normally defined as separate
itp files in topology.top) of the protein in case of its modeling
using MARTINI system. I have not found how to discriminate ( by
different colors of individual chains) using VMD (e.g bendix plugin)
because in CG representation there are alot of problem even with the
browsing of the sequence of the molecule.

Thanks so much for any ideas!

James
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