[gmx-users] Lipid Simulation Analysis

[Mr. Zaved Hazarika]

Hello

What kind of analysis can we perform for a lipid bilayer simulation? And
which are the tools available in gromacs to analyse bilayer simulation?

Thank You

Regards
Z. Hazarika
Research Scholar
Tezpur University
Tezpur


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[gmx-users] Positive potential energy

[Emran Heshmati]

Hi allI run two simulations on a 16 aa peptide under the same conditions 
(forcefield, simulation duration, ...) except the solvent in one of the 
simulations was TFE instead of water. The potential energy in the TFE 
containing system was positive (about 14 Kj/mol), while in water containing 
system was negative (about -7 Kj/mol). Is it normal? or some kind of error 
has occurred?  Best Regards
Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist
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[gmx-users] Positive potential energy

[Emran Heshmati]

Hi allI run two simulations on a 16 aa peptide under the same conditions 
(forcefield, simulation duration, ...) except the solvent in one of the 
simulations was TFE instead of water. The potential energy in the TFE 
containing system was positive (about 14 Kj/mol), while in water containing 
system was negative (about -7 Kj/mol). Is it normal? or some kind of error 
has occurred?  Best Regards
Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist
P Save a tree... please don't print this e-mail unless you really need to
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[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

[Tomasz Piskorz]

Dear all,

I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen
that the topology is already available in CHARMM-DrudeFF and I would like
to transfer it to GROMACS. However, I don't know how to calculate the
charge of Drude particle, which is required by topology in GROMACS. Does
anyone know how to do it?

Atomic polarizability can be described by equation:
alpha = (q_D)^2/k,
where k = 418400 kJ/(mol*nm^2) and alpha is given in CHARMM topology (i.g.
for O in glycine alpha=0.000651 nm^3). However, when I try to calculate the
charge I always get a wrong result. Is this question which I should use or
there is something more which I don't take under consideration?

With kind regards,
Tomasz K. Piskorz
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Re: [gmx-users] Lipid Simulation Analysis

[Nikhil Maroli]

Hi,
What kind of information do you want to find? There are numbers of stuff
you can do.
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[gmx-users] Doubt about constrained NM

[Varvdekar Bhagyesh Rajendra]

Dear all,

Is it possible to do constrained Normal Mode Analysis in Gromacs such as a free 
ligand buried in a constrained protein to study the effects of the binding on 
the normal modes of ligand? I had tried to used DPOSRES_A, as my protein is 
chain A, but everytime gromacs throws the error "Constraints present with 
Normal Mode Analysis, this combination is not supported". 

If indeed it is posssible, what are the suggested settings to be done in mdp 
file. If no, what are the suggested softwares that can do the same.

Thank you,

Best Regards,

Bhagyesh 
IIIT Hyderabad, India
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Re: [gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

[Justin Lemkul]

On 5/31/17 7:06 AM, Tomasz Piskorz wrote:

Dear all,

I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen
that the topology is already available in CHARMM-DrudeFF and I would like
to transfer it to GROMACS. However, I don't know how to calculate the
charge of Drude particle, which is required by topology in GROMACS. Does
anyone know how to do it?

Atomic polarizability can be described by equation:
alpha = (q_D)^2/k,
where k = 418400 kJ/(mol*nm^2) and alpha is given in CHARMM topology (i.g.
for O in glycine alpha=0.000651 nm^3). However, when I try to calculate the
charge I always get a wrong result. Is this question which I should use or
there is something more which I don't take under consideration?



Yes, there is an implicit conversion factor of Coulomb's constant.

qD = sqrt((alpha/kD)/CCELEC)

In CHARMM units, this is

qD = sqrt((0.651/1000)/332.0716)

I'll add the model compounds to the next release of the GROMACS-formatted Drude 
force field.  I have other issues to sort out before doing that, though.


-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 to perform final MD simulation after extending a NPT simulation

[Justin Lemkul]

On 5/30/17 8:50 PM, Adarsh V. K. wrote:

Dear all,

*I used following command to extend a NPT simulation*

gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v

*Now to do final MD simulation what command I should use?*

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v

or

gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
md_0_1.tpr
gmx mdrun -deffnm md_0_1 -v



I suggest you use gmx check to investigate the contents and differences between 
the checkpoint files.  If "npt" is the first part of the run, and "tpxout" is 
the second part, and you want to continue from the second part...


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] calculation of energy of individual water molecules in gromacs

[Justin Lemkul]

On 5/31/17 12:24 AM, Saumyak Mukherjee wrote:

Thanks Justin for the reply.

Supposing that I have 2300 (average) water molecules in a 1 nm hydration
shell around a protein, I need to calculate the interaction energy of each
and everyone of them in all the time frames, with the rest of the system. I
believe this is not possible using energygrps. Is there any other way?



That *is* possible with energygrps but you'll have to do each calculation 
separately using different groups.  Very tedious.


-Justin


On 31 May 2017 at 05:39, Justin Lemkul  wrote:




On 5/30/17 1:52 AM, Saumyak Mukherjee wrote:


Dear users,

I need to calculate the energy of individual water molecules in a 1 nm
shell around protein. That is, there will be n number of energy terms in
each time frame if there are n number of water molecules in the said
hydration shell at that time step. Is there a way to do it in GROMACS?



The internal energy of a water molecule?  If you're using standard rigid
waters, that quantity is by definition zero.  Interaction energy is another
matter and can be calculated using energygrps.  Whether or not that's
useful depends on the force field, as I just commented in another thread.

-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] Need to confirm parameters.

[Justin Lemkul]

On 5/31/17 2:26 AM, Sailesh Bataju wrote:

Extract the coordinates of any valine side chain in a protein, make an IBUT .hdb
entry based off of it (all you'll need to do is change 2 -> 3 in the number of H
added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms
for you.



-Justin


I did exactly you said and topology files were generated. The output
of the terminal is:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading test2_edited.pdb...
Read 'ALKANE ISOMER OF N-BUTANE', 13 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 13 atoms

   chain  #res #atoms
   1 'A' 1 13

All occupancies are one
Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 412
Reading residue database... (charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.rtp
Residue 1025
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.5#
Processing chain 1 'A' (13 atoms, 1 residues)
Warning: Starting residue IBU1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 14 atoms
Making bonds...
Number of bonds was 13, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   27 dihedrals,0 impropers,   24 angles
 27 pairs,   13 bonds and 0 virtual sites
Total mass 58.124 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: test2_edited.pdb.
The Charmm36 force field and the tip3p water model are used.
- ETON ESAELP 

But the topol.top file looks empty. The topol.top file is:

; Include forcefield parameters
#include "charmm36.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
Alkane_chain_A  3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   1 IBU rtp IBU  q  0.0
  1  CC31A  1IBU CT  1  -0.09 12.011
; qtot -0.09
  2  HCA1A  1IBU HT  2   0.09  1.008   ; qtot 0
  3  CC33A  1IBU C1  3  -0.27 12.011
; qtot -0.27
  4  HCA3A  1IBUH11  4   0.09  1.008
; qtot -0.18
  5  HCA3A  1IBUH12  5   0.09  1.008
; qtot -0.09
  6  HCA3A  1IBUH13  6   0.09  1.008   ; qtot 0
  7  CC33A  1IBU C2  7  -0.27 12.011
; qtot -0.27
  8  HCA3A  1IBUH21  8   0.09  1.008
; qtot -0.18
  9  HCA3A  1IBUH22  9   0.09  1.008
; qtot -0.09
 10  HCA3A  1IBUH23 10   0.09  1.008   ; qtot 0
 11  CC33A  1IBU C3 11  -0.27 12.011
; qtot -0.27
 12  HCA3A  1IBUH31 12   0.09  1.008
; qtot -0.18
 13  HCA3A  1IBUH32 13   0.09  1.008
; qtot -0.09
 14  HCA3A  1IBUH33 14   0.09  1.008   ; qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
 1 2 1
 1 3 1
 1 7 1
 111 1
 3 4 1
 3 5 1
 3 6 1
 7 8 1
 7 9 1
 710 1
1112 1
1113 1
1114 1

[ pairs ]
;  aiaj functc0c1c2c3
 2 4 1
 2 5 1
 2 6 1
 2 8 1
 2 9 1
 210 1
 212 1
 213 1
 214 1
 3 8 1
 3 9 1
 310 1
 312 1
 313 1
 314 1
 4 7 1
 411 1
 5 7 1
 511 1
 6 7 1
 611 1
 712 1
 713 1
 714 1
 811 1
 911 1
1011 1

[ angles ]
;  aiajak funct  

Re: [gmx-users] Atom type CB ERROR

[Justin Lemkul]

On 5/31/17 1:18 AM, Kashif wrote:

I got parameter file (ligand.par) from swissparam. What should I add from
this file and where? means the topol.top file created during the
simulation, should I use that file to include CB parameter? Please find the
parameter data generated from swiss para and help me what to add regarding
CB atom type.



These are all new parameters, so you need all of them. Hopefully it also 
supplied you with nonbonded parameters for all those types.  I'm sure it did, 
but I have no experience with SwissParam.


-Justin


* 
* Built parameters for ligand.mol2
*by user vzoete Mon May 29 09:38:13 CEST 2017
* 
*
BONDS
HCMM CB381.853 1.0840
HCMM CR342.991 1.0930
HCMM C=O   334.643 1.1010
HCMM C=C   372.066 1.0830
CR   CR306.432 1.5080
CR   NC=O  335.651 1.4360
CR   NC=C  354.218 1.4460
NC=O C=O   419.491 1.3690
CR   CB356.737 1.4860
CB   CB401.068 1.3740
C=O  CB322.985 1.4570
C=O  O=C   931.963 1.2220
NC=C C5B   478.144 1.3510
C=C  NPYL  443.600 1.3680
C=C  CB360.335 1.4490
C=C  C=C   684.039 1.3330
NPYL N5A   396.750 1.3390
NPYL C5A   453.459 1.3640
N5A  C5B   594.297 1.3350
C5B  N5B   320.682 1.3690
CSP  CB391.856 1.4240
CSP  NSP   1193.344 1.1600
C5A  N5B   599.191 1.3130
C5A  N=C   491.098 1.3450
C=O  N=C   725.204 1.2900
C=O  C=C   328.526 1.4680

ANGLES
CB   CB   CB 48.145119.9770
CB   CB   HCMM   40.517120.5710
CB   CB   CR 57.788120.4190
CB   CB   C=O57.429114.4750
NPYL C=C  CB 71.966120.
NPYL C=C  C=C70.239122.3600
CB   C=C  C=C43.035117.5080
C=C  NPYL N5A64.769133.2200
C=C  NPYL C5A61.747130.2750
N5A  NPYL C5A92.404112.0870
NPYL N5A  C5B   125.076101.5500
N5A  C5B  N5B75.924115.3690
N5A  C5B  NC=C   68.943129.1250
N5B  C5B  NC=C   71.966120.
C=C  CB   CB 51.240119.6950
NPYL C5A  N5B72.829110.8650
NPYL C5A  N=C76.859121.7410
N5B  C5A  N=C65.633133.0200
C5B  N5B  C5A86.791103.7790
N=C  C=O  C=C59.803122.2530
N=C  C=O  HCMM   44.835119.4910
C=C  C=O  HCMM   64.841115.3500
C5A  N=C  C=O89.741109.9890
CB   CB   CSP65.201119.6140
C=C  C=C  C=O39.221111.2970
C=C  C=C  HCMM   38.502121.0040
C=O  C=C  HCMM   35.047117.2910
HCMM CR   HCMM   37.134108.8360
HCMM CR   CR 45.770110.5490
HCMM CR   NC=O   53.255107.6460
CR   CR   NC=O   75.564109.9600
HCMM CR   NC=C   51.743109.8700
CR   CR   NC=C   81.321108.6780
CR   NC=O C=O59.084119.6000
CR   NC=O CR 80.386117.9090
CB   CR   HCMM   45.122109.4910
CB   CR   CR 54.406108.6170
CR   CR   CR 61.243109.6080
CB   C=O  NC=O   79.234112.4950
CB   C=O  O=C52.823119.9680
NC=O C=O  O=C65.273127.1520
C5B  NC=C CR 76.571115.4830
CR   NC=C CR 76.571113.7030
CB   CSP  NSP33.968180.

DIHEDRALS
CB   CB   CB   CB   3.500  2   180.00
CB   CB   CB   HCMM 3.500  2   180.00
CB   CB   C=O  NC=O 1.250  2   180.00
CB   CB   C=O  O=C  1.250  2   180.00
CB   CB   CSP  NSP  0.000  1 0.00
CB   CB   CR   HCMM-0.210  2   180.00
CB   CB   CR   HCMM 0.196  3 0.00
CB   CB   CR   CR   0.225  2   180.00
CB   CB   CB   C=C  3.500  2   180.00
CB   CR   CR   HCMM 0.195  3 0.00
CB   CR   CR   CR   0.150  3 0.00
CB   CB   CB   CSP  3.500  2   180.00
CB   C=O  NC=O CR   3.000  2   180.00
C=C  NPYL N5A  C5B  0.000  1 0.00
C=C  NPYL C5A  N5B  3.000  2   180.00
C=C  NPYL C5A  N=C  3.000  2   180.00
C=C  CB   CB   HCMM 1.000  2   180.00
C=C  C=C  C=O  N=C  1.250  2   180.00
C=C  C=C  C=O  HCMM 1.250  2   180.00
NPYL C=C  CB   CB   1.000  2   180.00
NPYL C=C  C=C  C=O  0.900  2   180.00
NPYL C=C  C=C  HCMM 0.900  2   180.00
NPYL N5A  C5B  N5B  3.500  2   180.00
NPYL N5A  C5B  NC=C 3.500  2   180.00
NPYL C5A  N5B  C5B  3.500  2   180.00
NPYL C5A  N=C  C=O  0.900  2   180.00
N5A  NPYL C=C  CB   3.000  2   180.00
N5A  NPYL C=C  C=C  3.000  2   180.00
N5A  NPYL C5A  N5B  2.000  2   180.00
N5A  NPYL C5A  N=C  2.000  2   180.00
N5A  C5B  N5B  C5A  3.500  2   180.00
N5A  C5B  NC=C CR   1.800  2   180.00
C5B  N5A  NPYL C5A  2.000  2   180.00
C5B  N5B  C5A  N=C  3.500  2   180.00
C5B  NC=C CR   HCMM 0.125  3 0.00
C5B  NC=C CR   CR   0.125  3 0.00
CB   CB   CB   CR   3.500  2   180.00
CB   CB   C=C  C=C  1.000  2   180.00
CB   C=C  NPYL C5A  3.000  2   180.00
CB   C=C  C=C  C=O  0.900  2   180.00
CB   C=C  C=C  HCMM 0.900  2   180.00
C5A  NPYL C=C  C=C  3.000  2   180.00
C5A  N5B  C5B  NC=C 3.500  2   180.00
C5A  N=C  C=O  C=C  0.900  2   180.00
C5A  N=C  C=O  HCMM 0.900  2   180.00
N5B  C5B  NC=C CR   1.800  2   180.00
N5B  C5A  N=C  C=O  

[gmx-users] Simulated annealing

[Venkat Raman]

Hi all,
   I am using Gromacs version 4.5.6 for peptide simulation. The
structure of the peptide (16mer) was predicted from Pepfold3 server. I did
Simulated annealing so that the side chains get properly oriented and the
predicted structure will reach its global optimum so that the structure
becomes more stable for production run. I have doubt in the mdp paramteres
regarding position restraints and the annealing time and temperature. I
tried with position restraints so that the backbone is restrained and the
side chains are free to move. The annealing was pretty good. I did SA after
NVT. I dont know to proceed further. How to finalize the mdp parameters
like pressure couping and generate velocities for simulated annealing?

Thanks in advance.
K.L. Venkatraman
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Re: [gmx-users] Reg: creation of separate chains in .pdb file

[Syed Azeem]

> On 5/29/17 8:00 AM, Syed Azeem wrote:
>> Hey all,
>>
>> I simulated a protein-peptide docked complex. Post simulation, I
>> created an index file selecting only the Protein Group
>> (protein-peptide complex). Then using editconf, I created a .pdb file
>> for the same.
>>
>> When I view the prtn.pdb file, only the protein is available but not
>> the peptide. Still the prtn.pdb file has coordinates for peptide as
>> well. The pdb file also lacks a chain identifier, which was present in
>
> If you're having trouble viewing the coordinates, that's a problem with the
>
> viewer itself.  You say that the coordinates are there (as they should be)
> so
> there's no reason they can't be visualized if rendered properly.
>
>> the initial structure.
>>
>> How to overcome this?
>>
>
> Add suitable chain identifiers back into the coordinate file.

Hey Justin,

I tried adding chain identifiers naming A & B to the file. It creates
another linear peptide chain away from main complex, when I view it in
Pymol.

>
> -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] Reg: creation of separate chains in .pdb file

[Justin Lemkul]

On 5/31/17 8:26 AM, Syed Azeem wrote:

On 5/29/17 8:00 AM, Syed Azeem wrote:

Hey all,

I simulated a protein-peptide docked complex. Post simulation, I
created an index file selecting only the Protein Group
(protein-peptide complex). Then using editconf, I created a .pdb file
for the same.

When I view the prtn.pdb file, only the protein is available but not
the peptide. Still the prtn.pdb file has coordinates for peptide as
well. The pdb file also lacks a chain identifier, which was present in


If you're having trouble viewing the coordinates, that's a problem with the

viewer itself.  You say that the coordinates are there (as they should be)
so
there's no reason they can't be visualized if rendered properly.


the initial structure.

How to overcome this?



Add suitable chain identifiers back into the coordinate file.


Hey Justin,

I tried adding chain identifiers naming A & B to the file. It creates
another linear peptide chain away from main complex, when I view it in
Pymol.



Sounds like a periodicity issue.  PyMOL is only telling you what's there; it's 
not "creating" anything :)


-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] Doubt about gmx wham analysis

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the ligand 
is pulled along the COM of two groups protein-ligand in all directions to 
calculate binding affinity using umbrella sampling. On the other hand, the 
tutorials use pull_coord1_dim = N N Y. Hence, I concluded my reaction 
coordinate differs as mentioned in the help menu of gmx wham : "If you have 
some unusual  reaction coordinate you may also generate your own .pdo files and 
feed them with the -ip option into to gmx wham"

Also, the following warning is thrown by gmx wham: " WARNING, no data point in 
bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your 
histograms! "
I was not sure if the z corresponds to the coordinate axis or just the z-axis 
(which was not the only reaction coordinate in my system).

All this made me conclude that the pullx files are not enough and the so called 
pdo files must be necessary, hence the doubt arised. I would appreciate if some 
more light is shed in this area.

Thank you for the help in answering the doubt.

Best Regards,
Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Wednesday, May 31, 2017 5:42:52 AM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/30/17 6:49 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
> 
> I have followed the Umbrella sampling tutorial 
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
>  on a Protein-ligand system using gromacs 5.1.1 while making some changes in 
> md_pull code with pull_coord1_dim = Y Y Y . Now I have to perform WHAM 
> analysis using gmx wham. As my system (Protein-ligand system) has the 
> reaction coordinate as the center of masses between the protein and ligand I 
> have to supply the .pdo file as suggested in gmx wham help menu. I would 
> appreciate if anyone could help me to generate these pdo files because I have 
> not encountered any option to generate them.
> 

.pdo files were umbrella sampling output files from ancient versions of 
GROMACS. 
  Support for their interpretation is maintained only for backwards 
compatibility.

Look through the tutorial again; nowhere does it use .pdo files and yet it 
still 
calculates a PMF :)

-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] Doubt about gmx wham analysis

[Justin Lemkul]

On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the ligand is pulled 
along the COM of two groups protein-ligand in all directions to calculate binding 
affinity using umbrella sampling. On the other hand, the tutorials use pull_coord1_dim = 
N N Y. Hence, I concluded my reaction coordinate differs as mentioned in the help menu of 
gmx wham : "If you have some unusual  reaction coordinate you may also generate your 
own .pdo files and feed them with the -ip option into to gmx wham"



The fact that your reaction coordinate is different from the tutorial is 
irrelevant.  You have an absolutely normal reaction coordinate and does not 
apply to what the gmx wham help text is talking about (which is probably a very 
outdated note at this point, given the massive changes in the pull code in 
recent versions).



Also, the following warning is thrown by gmx wham: " WARNING, no data point in bin 7 
(z=0.403502) ! You may not get a reasonable profile. Check your histograms! "
I was not sure if the z corresponds to the coordinate axis or just the z-axis 
(which was not the only reaction coordinate in my system).



It is the length along zeta, the reaction coordinate.  Don't confuse it with the 
z-axis, it's just shorthand.



All this made me conclude that the pullx files are not enough and the so called 
pdo files must be necessary, hence the doubt arised. I would appreciate if some 
more light is shed in this area.



You need better sampling, not archaic file formats.

-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] Doubt about gmx wham analysis

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

Many Thanks for the swift reply and the help in answering my doubts.

Best Regards,
Bhagyesh  

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Wednesday, May 31, 2017 6:06:59 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the 
> ligand is pulled along the COM of two groups protein-ligand in all directions 
> to calculate binding affinity using umbrella sampling. On the other hand, the 
> tutorials use pull_coord1_dim = N N Y. Hence, I concluded my reaction 
> coordinate differs as mentioned in the help menu of gmx wham : "If you have 
> some unusual  reaction coordinate you may also generate your own .pdo files 
> and feed them with the -ip option into to gmx wham"
> 

The fact that your reaction coordinate is different from the tutorial is 
irrelevant.  You have an absolutely normal reaction coordinate and does not 
apply to what the gmx wham help text is talking about (which is probably a very 
outdated note at this point, given the massive changes in the pull code in 
recent versions).

> Also, the following warning is thrown by gmx wham: " WARNING, no data point 
> in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your 
> histograms! "
> I was not sure if the z corresponds to the coordinate axis or just the z-axis 
> (which was not the only reaction coordinate in my system).
> 

It is the length along zeta, the reaction coordinate.  Don't confuse it with 
the 
z-axis, it's just shorthand.

> All this made me conclude that the pullx files are not enough and the so 
> called pdo files must be necessary, hence the doubt arised. I would 
> appreciate if some more light is shed in this area.
> 

You need better sampling, not archaic file formats.

-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] Lipid Simulation Analysis

[Mr. Zaved Hazarika]

Hello Nikhil Maroli

Basically I am new to lipid bilayer simulation. As of now I don't have any
particular objective. I am trying to learn lipid bilayer simulation.
Any suggestion would be great.

How can I check the stability of my simulated bilayer?


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Re: [gmx-users] calculation of energy of individual water molecules in gromacs

[Saumyak Mukherjee]

Thanks a lot for your comments.

I am doing the calculations using a self-written FORTRAN code.

On 31 May 2017 at 17:23, Justin Lemkul  wrote:

>
>
> On 5/31/17 12:24 AM, Saumyak Mukherjee wrote:
>
>> Thanks Justin for the reply.
>>
>> Supposing that I have 2300 (average) water molecules in a 1 nm hydration
>> shell around a protein, I need to calculate the interaction energy of each
>> and everyone of them in all the time frames, with the rest of the system.
>> I
>> believe this is not possible using energygrps. Is there any other way?
>>
>>
> That *is* possible with energygrps but you'll have to do each calculation
> separately using different groups.  Very tedious.
>
> -Justin
>
>
> On 31 May 2017 at 05:39, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/30/17 1:52 AM, Saumyak Mukherjee wrote:
>>>
>>> Dear users,

 I need to calculate the energy of individual water molecules in a 1 nm
 shell around protein. That is, there will be n number of energy terms in
 each time frame if there are n number of water molecules in the said
 hydration shell at that time step. Is there a way to do it in GROMACS?


 The internal energy of a water molecule?  If you're using standard rigid
>>> waters, that quantity is by definition zero.  Interaction energy is
>>> another
>>> matter and can be calculated using energygrps.  Whether or not that's
>>> useful depends on the force field, as I just commented in another thread.
>>>
>>> -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
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>>>
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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
>
> ==
> --
> Gromacs Users mailing list
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>



-- 

*Saumyak Mukherjee*

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

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

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Re: [gmx-users] Doubt about gmx wham analysis

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

During the pulling part of the umbrella sampling for finding binding affinity 
of the Protien-ligand system, the ligand(peptide) is deformed and its helices 
straighten along with large conformational changes in Protein. This is when the 
pull_coord1_dim = Y Y Y. But when I had used pull_coord1_dim = N N Y for one of 
the systems the peptide helices didn't deform. Is it reasonable for the ligand 
helices to deform when finding properties like Binding affinity? 

Can it be avoided if the ligand orientation is not known and using 
pull_coord1_dim = Y Y Y is necessary.

Best Regards,
Bhagyesh

- Original Message -
From: "Varvdekar Bhagyesh Rajendra" 
To: gmx-us...@gromacs.org
Sent: Wednesday, May 31, 2017 6:42:41 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin,

Many Thanks for the swift reply and the help in answering my doubts.

Best Regards,
Bhagyesh  

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Wednesday, May 31, 2017 6:06:59 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the 
> ligand is pulled along the COM of two groups protein-ligand in all directions 
> to calculate binding affinity using umbrella sampling. On the other hand, the 
> tutorials use pull_coord1_dim = N N Y. Hence, I concluded my reaction 
> coordinate differs as mentioned in the help menu of gmx wham : "If you have 
> some unusual  reaction coordinate you may also generate your own .pdo files 
> and feed them with the -ip option into to gmx wham"
> 

The fact that your reaction coordinate is different from the tutorial is 
irrelevant.  You have an absolutely normal reaction coordinate and does not 
apply to what the gmx wham help text is talking about (which is probably a very 
outdated note at this point, given the massive changes in the pull code in 
recent versions).

> Also, the following warning is thrown by gmx wham: " WARNING, no data point 
> in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your 
> histograms! "
> I was not sure if the z corresponds to the coordinate axis or just the z-axis 
> (which was not the only reaction coordinate in my system).
> 

It is the length along zeta, the reaction coordinate.  Don't confuse it with 
the 
z-axis, it's just shorthand.

> All this made me conclude that the pullx files are not enough and the so 
> called pdo files must be necessary, hence the doubt arised. I would 
> appreciate if some more light is shed in this area.
> 

You need better sampling, not archaic file formats.

-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] System volume "jumps" on exact continuations

[Elizabeth Ploetz]

Dear GMX-USERS,

We are observing abrupt, discontinuous “jumps” in our simulation box volume for 
different chunks of trajectory when performing exact continuations of standard, 
explicit solvent, MD simulations in the NPT ensemble. Note that these volume 
jumps do not appear to occur after every single continuation (there seems to be 
some element of randomness); however, they occur at some point in almost all of 
our different simulations. There are no visually apparent problems with the 
trajectories upon viewing them in e.g., Pymol. We are not able to visualize 
anything unusual, such as “bubbles” for cases where the system volume jumps to 
larger values.

Here is what we have tested:


  *   Temperature/Pressure Coupling Methods: Nosé-Hoover/Parrinello-Rahman and 
Berendsen/Berendsen are both affected
  *   Gromacs Versions: 4.6, 4.6.1, 5.0, and 2016 are all affected
  *   Machines/Architectures: three different clusters (we don’t know of a 
machine where it does not occur) are all affected:
 *   the lab’s cluster where we installed Gromacs ourselves
 *   the university cluster where Gromacs was installed by the university 
IT staff
 *   the Hansen cluster at Purdue, which we access only through a GUI at 
the DiaGrid portal
  *   Systems: Pure water systems as well as solvated single solute systems 
where the solute is a single protein, LJ sphere, or buckminsterfullerene are 
all affected
  *   Force fields: versions of AMBER, CHARMM, GROMOS, and OPLS force fields 
are all affected
  *   Box shape: cubic boxes and rhombic dodecahedrons are both affected
  *   Continuation method: Restarts of killed simulations (killed on purpose to 
increase the numbers of nodes as resources became available -- we don't do this 
anymore, but this was how we first saw the problem) and exact continuations of 
completed simulations are both affected
  *   Number of Nodes: We were almost convinced that it happened whenever we 
ran on >1 node (our usual situation), but not if we ran on 1 node only. We did 
some tests on one node on the lab’s cluster with and without MPI, to see 
whether or not it was MPI. System volume jumps were not (yet?) observed 
regardless of whether or not MPI was used. However, on the university cluster, 
we did tests of 24 processors using "-pe mpi-fill 24". Usually the 24 
processors were spread across >1 node, but sometimes they completely filled one 
node. There was one instance where there was a system volume jump when the 24 
processors changed from being distributed across >1 node to being on 1 node 
only. However, MPI was used in all of those simulations. So, we still have not 
proved that it is not MPI that is a problem. Unfortunately, this test result is 
still murky. Perhaps we should not have even mentioned it.
  *   Cut-off Scheme: We have done significantly fewer simulations with the 
Verlet cut-off scheme; however, so far the system volume jumps have not 
occurred with Verlet. We are continuing these tests.

Here is how we do exact continuations:
gmx_mpi convert-tpr -s previous.tpr -extend 2 -o next.tpr
mpiexec gmx_mpi mdrun -v -deffnm next -cpi previous.cpt -noappend >& myjob

Here
 is an example (CHARMM22*-based) MDP file (only used for the initial production 
run).

We have performed the Gromacs regression tests (with one processor, >1 
processor but only 1 node, and with more processors than will fit on one node) 
on the two machines that we have command line access to (lab and university 
clusters). Some of the regression tests reset the number of processors to 8 and 
thus are running on only one node. But, for what it is worth, all tests passed.

A linked Photobucket 
image
 shows the same system ran for five 1-ns chunks with exact continuations on 2 
machines: the university's or the lab's cluster. In Row 1, note that a 
particular system box volume is obtained on the university cluster with 1 node 
and MPI. No system volume jumps are noted. However, the average volume is not 
the same when ran on the lab’s cluster with 3 nodes, and a system volume jump 
occurs at 2ns (2nd Row). The system volume does at least roughly match that of 
the university cluster when ran on the lab's cluster with 1 node, both without 
(3rd Row) or with (4th Row) MPI.

Some may view these as small volume jumps, but they correspond to the volume of 
many water molecules (1 water has a volume of ~0.03 nm3). Often the volume 
jumps are larger than those shown in the linked figure (e.g., ~7 nm3).

When a jump occurs, the system stays at that new volume; it is not a "blip" 
that then re-adjusts to the original volume. These volume jumps seem suggestive 
of changes to the simulation settings or FF parameters occurring during the 
continuations.

We would greatly appreciate any advice. Uncertainty of the system volume 
pr

Re: [gmx-users] Deuterium Order Parameter Calculations

[Sanim Rahman]

Thank you Justin,

That makes much more sense. I was able to fix the error. I have one more
question that is out of topic from the original question. Is there a guide
that informs the user on what index groups should be made for each type of
analysis? I am also trying to use gmx_potential to do electrostatic
potential on a membrane solvated in KCl. If I want to do this, what index
group would I use?

Regards,
Sanim Rahman



On Tue, May 30, 2017 at 8:13 PM, Justin Lemkul  wrote:

>
>
> On 5/30/17 7:16 PM, Sanim Rahman wrote:
>
>> Hello everyone,
>>
>> I have a question about calculating Deuterium Order Parameters using
>> g_order. Is it common to get unrealistic values for Scd if you have not
>> run
>> the simulation long enough (over 25 ns?)? I ran the calculations after
>> equilibration on a POPC bilayer just to experiment with the command and I
>> received "NaN" values for two of my carbons for my calculations on Sn1.
>>
>>
> This means something is wrong with your inputs, likely incorrectly
> specified index groups.
>
> -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
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Re: [gmx-users] Lipid Simulation Analysis

[Daniel Bauer]

Hello,


First of all you can try to reproduce basic lipid properties as the area
per lipid and bilayer thickness. Both can be easily calculated from the
position of lipid headgroups.

Other useful properties is the diffusion rate of lipids (accessable by
calculating the mean square displacement) and the deuterium order.


Best regards!


On 31.05.2017 15:39, Mr. Zaved Hazarika wrote:
> Hello Nikhil Maroli
>
> Basically I am new to lipid bilayer simulation. As of now I don't have any
> particular objective. I am trying to learn lipid bilayer simulation.
> Any suggestion would be great.
>
> How can I check the stability of my simulated bilayer?
>
>
> ___
> D I S C L A I M E R
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and
> destroy it from your system. Though considerable effort has been made to 
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> or error-free as information could be intercepted, corrupted, lost, 
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> delayed, or may contain viruses. The recipient must verify the integrity of 
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>

-- 
Don't trust atoms, they make up everything.

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[gmx-users] AMBER LIPID14 ff in GROMACS

[Amit Singh]

Is there any way to use Amber Lipid14 force field parameters for GROMACS
-- 
सस्नेह / with regards
अमित सिंह / Amit Singh
कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied Sciences
पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
बठिंडा / Bathinda 151 001
भारत / INDIA
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Re: [gmx-users] System volume "jumps" on exact continuations

[Christopher Neale]

1. Once you identify a continuation (with associated run script) that gives the 
discontinuity, if you run many repeats of the original continuation then does 
the jump always occur or only sometimes?


2. Did you do any of the MPI runs with -notunepme ? That would be my first 
suspect.


3. Did you try explicitly setting a relatively large rlist and set 
verlet-buffer-tolerance = -1 (both in the .mdp file)? That would be my second 
suspect, though you say you've never seen the problem with verlet cutoff-scheme 
so I guess this suggestion is not related to the underlying issue.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Elizabeth 
Ploetz 
Sent: 31 May 2017 10:56:30
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] System volume "jumps" on exact continuations

Dear GMX-USERS,

We are observing abrupt, discontinuous “jumps” in our simulation box volume for 
different chunks of trajectory when performing exact continuations of standard, 
explicit solvent, MD simulations in the NPT ensemble. Note that these volume 
jumps do not appear to occur after every single continuation (there seems to be 
some element of randomness); however, they occur at some point in almost all of 
our different simulations. There are no visually apparent problems with the 
trajectories upon viewing them in e.g., Pymol. We are not able to visualize 
anything unusual, such as “bubbles” for cases where the system volume jumps to 
larger values.

Here is what we have tested:


  *   Temperature/Pressure Coupling Methods: Nosé-Hoover/Parrinello-Rahman and 
Berendsen/Berendsen are both affected
  *   Gromacs Versions: 4.6, 4.6.1, 5.0, and 2016 are all affected
  *   Machines/Architectures: three different clusters (we don’t know of a 
machine where it does not occur) are all affected:
 *   the lab’s cluster where we installed Gromacs ourselves
 *   the university cluster where Gromacs was installed by the university 
IT staff
 *   the Hansen cluster at Purdue, which we access only through a GUI at 
the DiaGrid portal
  *   Systems: Pure water systems as well as solvated single solute systems 
where the solute is a single protein, LJ sphere, or buckminsterfullerene are 
all affected
  *   Force fields: versions of AMBER, CHARMM, GROMOS, and OPLS force fields 
are all affected
  *   Box shape: cubic boxes and rhombic dodecahedrons are both affected
  *   Continuation method: Restarts of killed simulations (killed on purpose to 
increase the numbers of nodes as resources became available -- we don't do this 
anymore, but this was how we first saw the problem) and exact continuations of 
completed simulations are both affected
  *   Number of Nodes: We were almost convinced that it happened whenever we 
ran on >1 node (our usual situation), but not if we ran on 1 node only. We did 
some tests on one node on the lab’s cluster with and without MPI, to see 
whether or not it was MPI. System volume jumps were not (yet?) observed 
regardless of whether or not MPI was used. However, on the university cluster, 
we did tests of 24 processors using "-pe mpi-fill 24". Usually the 24 
processors were spread across >1 node, but sometimes they completely filled one 
node. There was one instance where there was a system volume jump when the 24 
processors changed from being distributed across >1 node to being on 1 node 
only. However, MPI was used in all of those simulations. So, we still have not 
proved that it is not MPI that is a problem. Unfortunately, this test result is 
still murky. Perhaps we should not have even mentioned it.
  *   Cut-off Scheme: We have done significantly fewer simulations with the 
Verlet cut-off scheme; however, so far the system volume jumps have not 
occurred with Verlet. We are continuing these tests.

Here is how we do exact continuations:
gmx_mpi convert-tpr -s previous.tpr -extend 2 -o next.tpr
mpiexec gmx_mpi mdrun -v -deffnm next -cpi previous.cpt -noappend >& myjob

Here
 is an example (CHARMM22*-based) MDP file (only used for the initial production 
run).

We have performed the Gromacs regression tests (with one processor, >1 
processor but only 1 node, and with more processors than will fit on one node) 
on the two machines that we have command line access to (lab and university 
clusters). Some of the regression tests reset the number of processors to 8 and 
thus are running on only one node. But, for what it is worth, all tests passed.

A linked Photobucket 
image
 shows the same system ran for five 1-ns chunks with exact continuations on 2 
machines: the university's or the lab's cluster. In Row 1, note that a 
particular system box volume is obtained on the university cluster with 1 node 
and MPI. No system volume jumps are noted. However, the ave

Re: [gmx-users] System volume "jumps" on exact continuations

[Szilárd Páll]

On Wed, May 31, 2017 at 9:44 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> 1. Once you identify a continuation (with associated run script) that
> gives the discontinuity, if you run many repeats of the original
> continuation then does the jump always occur or only sometimes?
>
>
> 2. Did you do any of the MPI runs with -notunepme ? That would be my first
> suspect.
>

However, if most runs are group scheme, a quick check could show whether
jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated
during continuation at least whether they do use separate PME ranks
(because otherwise CPU-only runs don't tune).


>
>
> 3. Did you try explicitly setting a relatively large rlist and set
> verlet-buffer-tolerance = -1 (both in the .mdp file)? That would be my
> second suspect, though you say you've never seen the problem with verlet
> cutoff-scheme so I guess this suggestion is not related to the underlying
> issue.
>

If I understood correctly, it's only group scheme runs where this has been
observed, so it could be some newer feature/change that interacts badly
with the group scheme.

BTW, do you have any data with 4.5?

I'd suggest that (especially if if investigation of current data does not
reveal the reasons) pick a setup where you seemed to get the anomaly and
run with the same settings using the Verlet scheme lots of short runs with
restarts in a loop.


>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Elizabeth
> Ploetz 
> Sent: 31 May 2017 10:56:30
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] System volume "jumps" on exact continuations
>
> Dear GMX-USERS,
>
> We are observing abrupt, discontinuous “jumps” in our simulation box
> volume for different chunks of trajectory when performing exact
> continuations of standard, explicit solvent, MD simulations in the NPT
> ensemble. Note that these volume jumps do not appear to occur after every
> single continuation (there seems to be some element of randomness);
> however, they occur at some point in almost all of our different
> simulations. There are no visually apparent problems with the trajectories
> upon viewing them in e.g., Pymol. We are not able to visualize anything
> unusual, such as “bubbles” for cases where the system volume jumps to
> larger values.
>
> Here is what we have tested:
>
>
>   *   Temperature/Pressure Coupling Methods: Nosé-Hoover/Parrinello-Rahman
> and Berendsen/Berendsen are both affected
>   *   Gromacs Versions: 4.6, 4.6.1, 5.0, and 2016 are all affected
>   *   Machines/Architectures: three different clusters (we don’t know of a
> machine where it does not occur) are all affected:
>  *   the lab’s cluster where we installed Gromacs ourselves
>  *   the university cluster where Gromacs was installed by the
> university IT staff
>  *   the Hansen cluster at Purdue, which we access only through a GUI
> at the DiaGrid portal
>   *   Systems: Pure water systems as well as solvated single solute
> systems where the solute is a single protein, LJ sphere, or
> buckminsterfullerene are all affected
>   *   Force fields: versions of AMBER, CHARMM, GROMOS, and OPLS force
> fields are all affected
>   *   Box shape: cubic boxes and rhombic dodecahedrons are both affected
>   *   Continuation method: Restarts of killed simulations (killed on
> purpose to increase the numbers of nodes as resources became available --
> we don't do this anymore, but this was how we first saw the problem) and
> exact continuations of completed simulations are both affected
>   *   Number of Nodes: We were almost convinced that it happened whenever
> we ran on >1 node (our usual situation), but not if we ran on 1 node only.
> We did some tests on one node on the lab’s cluster with and without MPI, to
> see whether or not it was MPI. System volume jumps were not (yet?) observed
> regardless of whether or not MPI was used. However, on the university
> cluster, we did tests of 24 processors using "-pe mpi-fill 24". Usually the
> 24 processors were spread across >1 node, but sometimes they completely
> filled one node. There was one instance where there was a system volume
> jump when the 24 processors changed from being distributed across >1 node
> to being on 1 node only. However, MPI was used in all of those simulations.
> So, we still have not proved that it is not MPI that is a problem.
> Unfortunately, this test result is still murky. Perhaps we should not have
> even mentioned it.
>   *   Cut-off Scheme: We have done significantly fewer simulations with
> the Verlet cut-off scheme; however, so far the system volume jumps have not
> occurred with Verlet. We are continuing these tests.
>
> Here is how we do exact continuations:
> gmx_mpi convert-tpr -s previous.tpr -extend 2 -o next.tpr
> mpiexec gmx_mpi mdrun -v -deffnm next -cpi previous.cpt -noappend >& myjob
>
> 

[gmx-users] REMD analysis of trajectories

[YanhuaOuyang]

Hi,
   I have run a 100ns-REMD of protein, which has 20 replicas (i.e. remd1.xtc, 
remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory at specific 
temperature  such as a trajectory at experiment temperature 298K rather than 
analyzing the continuous trajectory. I have known GROMACS exchange coordinate 
when REMD running. Do I just analyze remd2.xtc of replica 2(T=298K) if I want 
to analyze a trajectory at 298K? Do I need to do something else on the 
trajectories to get a trajectory at specific temperature(i.e. 298K)?

Best regards,
Ouyang
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