Re: [gmx-users] Need to confirm parameters.

[Sailesh Bataju]

>>* Making bonds...
*>>* Warning: Short Bond (5-1 = 0.025 nm)
*>>* Warning: Long Bond (5-6 = 0.99084 nm)
*>>* Warning: Long Bond (1-2 = 0.944378 nm)
*>>* Warning: Long Bond (1-3 = 0.895661 nm)
*>>* Warning: Long Bond (1-4 = 0.866986 nm)
*>>* Warning: Long Bond (7-8 = 0.502204 nm)
*>>* Warning: Long Bond (7-9 = 0.567317 nm)
*>> *Warning: Long Bond (7-10 = 0.92202 nm)
*>>* Warning: Long Bond (11-12 = 0.592831 nm)
*>>* Warning: Long Bond (11-13 = 0.700231 nm)
*>>* Warning: Long Bond (11-14 = 0.729592 nm)*

> The short bond warnings do, however, indicate that the starting geometry is 
> bad.

> -Justin

I'd a doubt about it you eventually pointed it out sir, thank you.
Those bond lengths have drastic differences than the bond lengths
given in ffbonded.itp file. Here it goes according to the .itp file:-

1-5 = 0.1538 nm

5-6 = 0. nm

1-2 = 0. nm

and so on...

Nothing has matched with those generated bonds. It looks like I've to
modify pdb file manually for correct geometry using distance formula
or is there some other way to do it, sir?

Thank you very much.
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[gmx-users] System Crashes

[Sheikh Imamul Hossain]

Hi Gromacs User,

I am running a big system consisting of more than 5000 CG lipids molecules
in each monolayer and these monolayers are separated by 133000 CG water
molecules in a box 50*50*100. Everything run well up to equilibration (5
equilibration for 10ns ) but after 3 microsecond production run the box
dimension reduces to  49.37048* 49.37048*11.52813. I am looking for the
reason why z dimension reduced? I am not sure is it fine or not. For your
consideration here is my mdp file that used for production run

; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
dt   = 0.03
nsteps   = 1
; number of steps for center of mass motion removal =
nstcomm  = 100
comm-grps = DPPC_POPC W

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 5000
; Output frequency for energies to log file and energy file =
nstlog   = 5000
nstenergy= 100
nstcalcenergy = 100
; Output frequency and precision for xtc file =
nstxtcout= 1000
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   = DPPC_POPC W

; NEIGHBORSEARCHING PARAMETERS =
cutoff-scheme= Verlet
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
verlet-buffer-tolerance  = 0.005
rlist = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = cutoff
coulomb-modifier = Potential-shift
rcoulomb = 1.2
rcoulomb-switch = 0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = cutoff
vdw-modifier = Potential-shift
rvdw = 1.2
rvdw-switch = 0.9
epsilon_rf   = 0

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = berendsen
nsttcouple = 2
; Groups to couple separately =
tc-grps  = DPPC_POPC W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0
ref_t= 310 310
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 12.0
compressibility  = 5e-5 5e-5
ref_p= 1.0  1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 310
gen_seed = 473529


; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4

; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30


...
If I change only the

Temperature coupling berendsen to V-rescale and the pressure coupling to as
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = surface-tension
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 12.0
compressibility  = 5e-5 0
ref_p= 400  1.0 ; (surface tension at 20mN/m)

without changing the other parameters  then the system crashes in it's
first equilibration with a massage

Atom 187258 moved more than the distance allowed by the domain
decomposition (1.202000) in direction X
distance out of cell 1.499496
New coordinates:   15.700   32.272   14.594
Old cell boundaries in direction X:0.000   14.432
New cell boundaries in direction X:0.000   14.200

How can I solve this problem?

N.B. Sorry for the lengthy message .

Sincerely Your’s
Sheikh Imamul Hossain
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[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

[Steffen Graether]

Hi,

I’ve tried installing GROMACS 2016.3 on Ubuntu 17.04. I’ve checked that gcc-6 
and g++6 are installed, but when running cmake  I get the following error:

-- Performing Test CXX11_STDLIB_PRESENT - Failed
CMake Error at cmake/gmxTestCXX11.cmake:139 (message):
  This version of GROMACS requires C++11-compatible standard library.  Please
  use a newer compiler, or a newer standard library, or use the GROMACS 5.1.x
  release.  See the installation guide for details.
Call Stack (most recent call first):
  CMakeLists.txt:164 (gmx_test_cxx11)

Searching for this problem I find a few references to having an up to date gcc, 
but nothing else. Can anyone point me in the right direction to fix this?

Thanks,
Steffen




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Re: [gmx-users] atomname2types.n2t explanation

[Justin Lemkul]

On 5/23/17 7:06 PM, Marcelo Depólo wrote:

Hi


Can someone explain what does each column on atomname2types.n2t mean?

For gromos53a5 it is:

H   H0.408  1.008  1  O 0.1
O   OA  -0.674 15.9994  2  C 0.14 H 0.1
C   CH3  0.000 15.0351  C 0.15
C   CH0  0.266 12.0114  C 0.15 C 0.15 C 0.15 O 0.14

I suppose the first column is the target atom name, the second is the atom
type, the third is charge and the fourth is mass.

Is the fifth the number of bonds? And the others?



You've got most of it right, but for the sake of being pedantic so someone can 
find it later:


1. Element name, which is used to match the first character in any supplied atom 
name

2. Atom type
3. Atom partial charge
4. Atom mass
5. Number of bonds formed by this atom
6 and onward: the elements and reference bond distances (N entries, where N is 
the number found in column 5)


Reference distances behave like any other in GROMACS, if not found within +/- 
10% they are not detected.


This information used to be on the wiki but got nuked; it will be added back to 
the documentation soon.


-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] Using CHARMM36 in GROMACS to simulate polysaccharides

[Justin Lemkul]

On 5/23/17 2:16 PM, Mohammad Hassan Khatami wrote:

Thank Justin!
I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight 
forward. However, while doing energy minimizations, I get several errors like 
the ones below, arise:

ERROR 2 [file topol.top, line 396]:
  No default U-B types
and
ERROR 5 [file topol.top, line 550]:
  No default Proper Dih. types

As it says, they might be related to the angles and dihedral parameters. Do you 
have any suggestion on where (and how) to add them?


You shouldn't need to add parameters, but without knowing what is on those lines 
(more specifically, the associated atom types because the atom numbers will mean 
nothing to me) there's nothing else I can say about it.  The entirety of the 
carbohydrate force field should already be ported over, so missing parameters 
are very odd.


-Justin


Thanks again,
MH


On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:

Hi Justin,
I am asked to focus on learning how to change and update the CHARMM36 
parameters, so I could implement the future changes and patches easier. (Thus, 
I am not focused in the Glycan Reader, at the moment.)

Thank you! I think I now have a better understanding of what should I do. For 
each part of my polymer,i.e. the initial, the middle and the final part, I have 
to modify the AGLC molecule to represent each of these parts, seperately.
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from 
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, 
I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in 
the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to 
it:


Note that your residue name must be limited to 4 characters so it can properly 
be read from the input coordinates.  AGLC14 won't work.


! equatorial-axial 1->4 linkage
PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC31610.09 !
ATOM 1O4  OC301-0.36 !
ATOM 2C1  CC31620.29 !
BOND 1O4  2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 
and C1 atoms. Then, I need to add the bond of

[ bond ]
…
O4  +C1



Correct.


Then, I need to apply  the bonds and angles parameters in the the 
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
!IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837

I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into 
the merged.vsd file, except for the PHI values. Where (and/or how) should I put 
it?
Am I on the right track?


You should not do this.  The .vsd file is for defining virtual sites.  The IC 
lines are for the CHARMM program's internal coordinate builder, specifying some 
optimized geometry (one that the force field in total should produce, or come 
very close).  All the bonded parameters you need are already in the force field 
because they come from the corresponding .prm files.  Do not adjust bonded 
parameter files.

-Justin



Thanks again for your help.
MH



On May 19, 2017, at 5:36 PM, Justin Lemkul > wrote:



On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file 
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.



Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.



Then, I might need to branch them with1->6 linkage.


Also totally possible.


I tried Glycan Reader, but itstill crashes.



Uploading a correctly named PDB file should work in Glycan Reader or the Quick MD 
Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, 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] Need to confirm parameters.

[Justin Lemkul]

On 5/23/17 8:03 AM, Sailesh Bataju wrote:

The easiest thing to do
(solving this issue and #1) is to create an isobutane .rtp entry and have
pdb2gmx do all the work for you.  It's very simple to do.



-Justin


Thank you sir, I've exactly followed your steps. I've created
isobutane.rtp file and modified residuetypes.dat file by adding IBUT
as Protein and then created PDB file from prodrg server. Then using
pdb2gmx command finally got this result:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading prodrg_ibut.pdb...
WARNING: all CONECT records are ignored
Read 14 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 14 atoms

  chain  #res #atoms
  1 ' ' 1 14


WARNING: there were 4 atoms with zero occupancy and 8 atoms with
 occupancy unequal to one (out of 14 atoms). Check your pdb file.

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/isobutane.rtp
Residue 1
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
Processing chain 1 (14 atoms, 1 residues)
Identified residue IBUT0 as a starting terminus.
Identified residue IBUT0 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
No suitable end (N or 5') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
No suitable end (C or 3') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
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...
Warning: Short Bond (5-1 = 0.025 nm)
Warning: Long Bond (5-6 = 0.99084 nm)
Warning: Long Bond (1-2 = 0.944378 nm)
Warning: Long Bond (1-3 = 0.895661 nm)
Warning: Long Bond (1-4 = 0.866986 nm)
Warning: Long Bond (7-8 = 0.502204 nm)
Warning: Long Bond (7-9 = 0.567317 nm)
Warning: Long Bond (7-10 = 0.92202 nm)
Warning: Long Bond (11-12 = 0.592831 nm)
Warning: Long Bond (11-13 = 0.700231 nm)
Warning: Long Bond (11-14 = 0.729592 nm)
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

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: prodrg_ibut.pdb.
The Charmm36 force field is used.
- ETON ESAELP 


1. According to the first warning like this "there were 4 atoms with
zero occupancy and 8 atoms with  occupancy unequal to one (out of 14
atoms)"

Is that a kind of error. Did I do any mistake as it said?



That's not an error and is irrelevant.

The short bond warnings do, however, indicate that the starting geometry is bad.


2. If i don't add IBUT as Protein in residuetypes.dat file I get error
like this however I get same topol.top file.

"Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (14 atoms, 1 residues)
Warning: Starting residue IBUT0 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

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)

Fatal error:
Residue 'IBUT' not found in residue topology database"

I've no idea whether I've successfully generated those files.



This fatal error has nothing to do with residuetypes.dat - it says that IBUT is 
not in the .rtp file.  But the above text says it completed successfully.  You 
don't need to denote IBUT as Protein, but there's no harm either way.


-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

==
--

[gmx-users] atomname2types.n2t explanation

[Marcelo Depólo]

Hi


Can someone explain what does each column on atomname2types.n2t mean?

For gromos53a5 it is:

H   H0.408  1.008  1  O 0.1
O   OA  -0.674 15.9994  2  C 0.14 H 0.1
C   CH3  0.000 15.0351  C 0.15
C   CH0  0.266 12.0114  C 0.15 C 0.15 C 0.15 O 0.14

I suppose the first column is the target atom name, the second is the atom
type, the third is charge and the fourth is mass.

Is the fifth the number of bonds? And the others?

Thanks in advance!
--
Marcelo
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 157, Issue 112

[Harry Ponce]

Thank you Mark and Szilárd! I have resorted to freezing the five atoms, and
that has seemed to work, but of course at an energy toll.

- Harrison

On Tue, May 23, 2017 at 3:55 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: (no subject) (Szil?rd P?ll)
>2. Applying Dihedral Restraints to Polymer in GROMACS 5.1
>   (Harry Ponce)
>3. Re: Using CHARMM36 in GROMACS to simulate polysaccharides
>   (Mohammad Hassan Khatami)
>4. mdrun failure (fatemeh ramezani)
>5. Re: Applying Dihedral Restraints to Polymer in GROMACS5.1
>   (Mark Abraham)
>
>
> --
>
> Message: 1
> Date: Tue, 23 May 2017 16:23:36 +0200
> From: Szil?rd P?ll 
> To: "Li, Zhixia" 
> Cc: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] (no subject)
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Please do not post questions to the list "owner" (=admin) address. Post
> your questions to the users' list instead.
>
> Are you sure you are using the MPI-enabled GROMACS installation? Look in
> the mdrun log header (posting the link to the whole log uploaded to some
> sharing service might also help identifying the issue).
>
> --
> Szil?rd
>
> On Sat, May 20, 2017 at 1:09 AM, Li, Zhixia  wrote:
>
> > Hi all,
> >
> > Recently, I want to try hybrid parallelization on two nodes with 12 cores
> > per node.  I want it to run 1 mpi per node and 12 openmp per mpi. The
> > command I use is:
> > mpirun -np 2 gmx_mpi mdrun -ntomp 12
> >
> > But I got the output like the following. It seems it only uses one node.
> > Does anyone know how to realize it? And is it the issue of compiling?
> Thank
> > you.
> >
> > Number of logical cores detected (12) does not match the number reported
> > by OpenMP (6).
> > Consider setting the launch configuration manually!
> >
> > Running on 1 node with total 12 cores, 12 logical cores
> > Hardware detected on host taub217 (the node of MPI rank 0):
> >   CPU info:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Xeon(R) CPU   X5650  @ 2.67GHz
> > SIMD instructions most likely to fit this hardware: SSE4.1
> > SIMD instructions selected at GROMACS compile time: SSE4.1
> >
> > Reading file em4.tpr, VERSION 5.1.4 (single precision)
> > The number of OpenMP threads was set by environment variable
> > OMP_NUM_THREADS to 12 (and the command-line setting agreed with that)
> > Using 2 MPI processes
> > Using 12 OpenMP threads per MPI process
> >
> >
> > WARNING: Oversubscribing the available 12 logical CPU cores with 24
> > threads.
> >  This will cause considerable performance loss!
> >
> > NOTE: Your choice of number of MPI ranks and amount of resources results
> > in using 12 OpenMP threads per rank, which is most likely inefficient.
> The
> > optimum i$
> >
> >
> > Non-default thread affinity set probably by the OpenMP library,
> > disabling internal thread affinity
> >
> >
> > Best,
> > Zhixia Li
> >
>
>
> --
>
> Message: 2
> Date: Tue, 23 May 2017 13:48:47 -0400
> From: Harry Ponce 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Applying Dihedral Restraints to Polymer in
> GROMACS 5.1
> Message-ID:
> 

Re: [gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1

[Mark Abraham]

Hi,

It's a restraint - they move in the context of the force field and your
extra potential. They're not frozen.

Mark

On Tue, May 23, 2017 at 7:49 PM Harry Ponce  wrote:

> Hello,
>
> I'm attempting to run an energy minimization on some high energy conformers
> of a polymer dimer while restraining two dihedral angles pertaining to the
> five backbone carbons of interest. The literature and forums online are
> sparse when it comes to non-biochemical systems, and it seems as though the
> syntax might have changed over the updated versions of GROMACS.
>
> I've attempted to implement this bit in my topology:
>
> #ifdef DIHRE
>
> [ dihedral_restraints ]
> ; ai   ajakal  type  label  phi  dphi  kfac  power
> 21 829 1  1  52  0 1  2
> 32 1 8 1  1  75  0 1  2
>
> #endif
>
> As well as this bit in my .mdp file:
>
> define= -DDIHRE
> ; Dihedral Restraints
> dihre= yes
> dihre_fc= 1000
> dihre_tau= 0.0
> nstdihreout= 50
>
> I've also tried using what I think is the more recent syntax for applying
> restraints:
>
> ; position restraints for System of UNNAMED
>
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
>21   1000   1000   1000
>31   1000   1000   1000
>81   1000   1000   1000
>   291   1000   1000   1000
>
> However, when I energy minimize and read the backbone dihedral angles they
> are different than the ones I started with! I am sure I have the correct
> atom numbers (1,2,3,8,29), but am not sure why GROMACS is reading them and
> then ignoring my restraints.
>
> Any ideas?
>
> Thank you very much,
> Harrison
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[gmx-users] mdrun failure

[fatemeh ramezani]

 Hi dear gmx-usersI am simulating gold surface- protein interaction by 
GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some 
freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun 
starts, temperature reaches to 5.50769e+05. md.mdp file containe:
title    = gold
cpp   = cpp
include   = 

; RUN CONTROL PARAMETERS
integrator   = md 
comm_mode  = Linear
;nstcomm   =  1
;comm_grps   = Protein  Non-protein 
;nstcalcenergy = 1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol   = 500.0
emstep    = 0.001
tinit  = 0.000
dt = 0.0005
nsteps  = 10

; OUTPUT CONTROL OPTIONS
nstxout = 3000
nstvout = 3000
nstfout  = 0
nstlog   = 1
nstenergy = 3000

; Output frequency and precision for xtc file
nstxtcout  = 3000
xtc-precision    = 3000



; NEIGHBORSEARCHING PARAMETERS
; Periodic boundary conditions: xyz (default), no (vacuum)
pbc  = xyz
periodic_molecules    = yes
; nblist cut-off    
rlist   = 1.10

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
r_coulomb    = 1.1
;pme_order   = 6
;fourierspacing   = 0.10
ewald_rtol    = 1e-06
ewald_geometry  = 3d

; Method for doing Van der Waals
vdw-type = switch
; cut-off lengths   
rvdw-switch   = 0.90
rvdw = 1.10

; OPTIONS FOR BONDS    
constraints   = none
constraint-algorithm  =  Lincs
lincs-order   = 8
lincs-iter   = 12
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 90

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl    = Nose-Hoover
nhchainlength   = 1
; Groups to couple separately
tc-grps = Protein  SOL NA CL     slab AUC 
; Time constant (ps) and reference temperature (K)
tau-t    =  0.2 0.2 0.2 0.2 0.2  0.2
ref-t =  300 300 300 300 300 300

; Non-equilibrium MD stuff
freezegrps    = slab
freezedim = Y Y Y

Can anyone help me to solve this problem?thank you in advance

Fatemeh Ramezani
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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

[Mohammad Hassan Khatami]

Thank Justin! 
I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight 
forward. However, while doing energy minimizations, I get several errors like 
the ones below, arise:

ERROR 2 [file topol.top, line 396]:
  No default U-B types
and 
ERROR 5 [file topol.top, line 550]:
  No default Proper Dih. types

As it says, they might be related to the angles and dihedral parameters. Do you 
have any suggestion on where (and how) to add them?
Thanks again,
MH
>> 
>> On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:
>>> Hi Justin,
>>> I am asked to focus on learning how to change and update the CHARMM36 
>>> parameters, so I could implement the future changes and patches easier. 
>>> (Thus, I am not focused in the Glycan Reader, at the moment.)
>>> 
>>> Thank you! I think I now have a better understanding of what should I do. 
>>> For each part of my polymer,i.e. the initial, the middle and the final 
>>> part, I have to modify the AGLC molecule to represent each of these parts, 
>>> seperately.
>>> So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch 
>>> from the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. 
>>> In this case, I need to create a new version of [ AGLC ] molecule (lets 
>>> call it [ AGLC14 ]) in the merged.rtp, with the changes below from the the 
>>> top_all36_carb.rtf, applied to it:
>> 
>> Note that your residue name must be limited to 4 characters so it can 
>> properly be read from the input coordinates.  AGLC14 won't work.
>> 
>>> ! equatorial-axial 1->4 linkage
>>> PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
>>> dele atom 1HO4
>>> dele atom 2HO1
>>> dele atom 2O1
>>> ATOM 1C4  CC31610.09 !
>>> ATOM 1O4  OC301-0.36 !
>>> ATOM 2C1  CC31620.29 !
>>> BOND 1O4  2C1
>>> I have to remove the HO4, HO1 and O1 lines and modify the values for the 
>>> C4, O4 and C1 atoms. Then, I need to add the bond of
>>> 
>>> [ bond ]
>>> …
>>> O4  +C1
>>> 
>> 
>> Correct.
>> 
>>> Then, I need to apply  the bonds and angles parameters in the the 
>>> top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS 
>>> CHARMM36.
>>> !IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
>>> IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
>>> IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
>>> IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
>>> IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837
>>> 
>>> I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values 
>>> into the merged.vsd file, except for the PHI values. Where (and/or how) 
>>> should I put it?
>>> Am I on the right track?
>> 
>> You should not do this.  The .vsd file is for defining virtual sites.  The 
>> IC lines are for the CHARMM program's internal coordinate builder, 
>> specifying some optimized geometry (one that the force field in total should 
>> produce, or come very close).  All the bonded parameters you need are 
>> already in the force field because they come from the corresponding .prm 
>> files.  Do not adjust bonded parameter files.
>> 
>> -Justin
>> 
>>> 
>>> Thanks again for your help.
>>> MH
>>> 
>>> 
 On May 19, 2017, at 5:36 PM, Justin Lemkul > wrote:
 
 
 
 On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:
> First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf 
> file I found different linkages for beta-glucose, but non for 
> alpha-glucose.
> I am trying to make a simple chain with 1->4 linkages like below:
> 
> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.
> 
 
 Linkages are not specific to the sugar; most are totally generic.  A few 
 comments suggest specific usage and may be corner cases, but your patches 
 will be among 14aa, 14ab, 14ba, 14bb.
 
> 
> Then, I might need to branch them with1->6 linkage.
 
 Also totally possible.
 
> I tried Glycan Reader, but itstill crashes.
> 
 
 Uploading a correctly named PDB file should work in Glycan Reader or the 
 Quick MD Simulator, but "still crashes" is not diagnostic of anything.  
 Specific help with CHARMM-GUI should be brought to their attention, though.
 
 -Justin
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[gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1

[Harry Ponce]

Hello,

I'm attempting to run an energy minimization on some high energy conformers
of a polymer dimer while restraining two dihedral angles pertaining to the
five backbone carbons of interest. The literature and forums online are
sparse when it comes to non-biochemical systems, and it seems as though the
syntax might have changed over the updated versions of GROMACS.

I've attempted to implement this bit in my topology:

#ifdef DIHRE

[ dihedral_restraints ]
; ai   ajakal  type  label  phi  dphi  kfac  power
21 829 1  1  52  0 1  2
32 1 8 1  1  75  0 1  2

#endif

As well as this bit in my .mdp file:

define= -DDIHRE
; Dihedral Restraints
dihre= yes
dihre_fc= 1000
dihre_tau= 0.0
nstdihreout= 50

I've also tried using what I think is the more recent syntax for applying
restraints:

; position restraints for System of UNNAMED

[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
   21   1000   1000   1000
   31   1000   1000   1000
   81   1000   1000   1000
  291   1000   1000   1000

However, when I energy minimize and read the backbone dihedral angles they
are different than the ones I started with! I am sure I have the correct
atom numbers (1,2,3,8,29), but am not sure why GROMACS is reading them and
then ignoring my restraints.

Any ideas?

Thank you very much,
Harrison
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Re: [gmx-users] (no subject)

[Szilárd Páll]

Please do not post questions to the list "owner" (=admin) address. Post
your questions to the users' list instead.

Are you sure you are using the MPI-enabled GROMACS installation? Look in
the mdrun log header (posting the link to the whole log uploaded to some
sharing service might also help identifying the issue).

--
Szilárd

On Sat, May 20, 2017 at 1:09 AM, Li, Zhixia  wrote:

> Hi all,
>
> Recently, I want to try hybrid parallelization on two nodes with 12 cores
> per node.  I want it to run 1 mpi per node and 12 openmp per mpi. The
> command I use is:
> mpirun -np 2 gmx_mpi mdrun -ntomp 12
>
> But I got the output like the following. It seems it only uses one node.
> Does anyone know how to realize it? And is it the issue of compiling? Thank
> you.
>
> Number of logical cores detected (12) does not match the number reported
> by OpenMP (6).
> Consider setting the launch configuration manually!
>
> Running on 1 node with total 12 cores, 12 logical cores
> Hardware detected on host taub217 (the node of MPI rank 0):
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Xeon(R) CPU   X5650  @ 2.67GHz
> SIMD instructions most likely to fit this hardware: SSE4.1
> SIMD instructions selected at GROMACS compile time: SSE4.1
>
> Reading file em4.tpr, VERSION 5.1.4 (single precision)
> The number of OpenMP threads was set by environment variable
> OMP_NUM_THREADS to 12 (and the command-line setting agreed with that)
> Using 2 MPI processes
> Using 12 OpenMP threads per MPI process
>
>
> WARNING: Oversubscribing the available 12 logical CPU cores with 24
> threads.
>  This will cause considerable performance loss!
>
> NOTE: Your choice of number of MPI ranks and amount of resources results
> in using 12 OpenMP threads per rank, which is most likely inefficient. The
> optimum i$
>
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
>
> Best,
> Zhixia Li
>
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Re: [gmx-users] Problem with accelerations

[Kamps, M.]

Mark,

I'm not really sure what you mean by technique. I assume NEMD stands
for Non-equilibrium MD? That is the case..

About my simulation: I am trying to simulate a fluid flow between
surfaces. Two atomistic surfaces of gold atoms have been created at
Z=0 and Z=z, where z is the top of the box. These surfaces are fixed.
In between is a fluid that should be accelerated in order to create a
flow. This is done by applying a constant acceleration in the X
direction via the commands; 'acc-grps = FLUID' and 'accelerate = 0.05
0 0'. Is this equal to the bug you referenced to?

Suppose the command is broken, does this mean that the simulation is
worthless since there are computational errors, or is the applied
velocity buggy but the results still useful? Suppose I can find the
right accelerations, can I still use the results?


Mark Abraham wrote:
> Hi,
> Which technique are you using for this?
> https://redmine.gromacs.org/issues/1354 speculates that this code is just
> broken, has been so for years, and should be removed given that nobody
> wishes to do the work to fix it ( :-( )
> Mark
> On Tue, May 23, 2017 at 11:13 AM Kamps, M.  wrote:
> > Dear GMX users,
> >
> > I have some strange behaviour which I cannot explain.
> >
> > I want to accelerate atoms through my box at a certain velocity. Since
> > I can only adjust the acceleration, I have to trial-and-error my way
> > to the right accelerations.
> >
> > To do this, I create a smaller 'testing' simulation, which is
> > continued from an extensive equilibrium. I apply an acceleration of
> > 0.05 nm/ps2, and after 200ps my velocity (gathered from gmx traj with
> > an gmx select input) says that the velocity is stable at around 0.04
> > nm/ps. throughout the simulation the velocity slightly increases due
> > to the atoms rearranging etc.
> >
> > Now I want to simulate the same behaviour, but for a longer amount of
> > time. I therefore take the exact same MDP file, and change nothing
> > except the time-related parameters. I change the number of total steps
> > and the timestep, but leave the acceleration intact. After analysing
> > the data I get a MUCH higher velocity! I can understand this due to
> > rearranging of the atoms on the longer term, but after the same 200ps
> > the velocity is also way higher.
> >
> > So during my smaller run the velocity was 0.04 nm/ps after 200 ps, in
> > this longer run, the velocity is 0.2 nm/ps after the same 200ps. How
> > is this possible? The exact same acceleration is applied.
> >
> > Am I missing something?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Problem with accelerations

[Mark Abraham]

Hi,

Which technique are you using for this?
https://redmine.gromacs.org/issues/1354 speculates that this code is just
broken, has been so for years, and should be removed given that nobody
wishes to do the work to fix it ( :-( )

Mark

On Tue, May 23, 2017 at 11:13 AM Kamps, M.  wrote:

> Dear GMX users,
>
> I have some strange behaviour which I cannot explain.
>
> I want to accelerate atoms through my box at a certain velocity. Since
> I can only adjust the acceleration, I have to trial-and-error my way
> to the right accelerations.
>
> To do this, I create a smaller 'testing' simulation, which is
> continued from an extensive equilibrium. I apply an acceleration of
> 0.05 nm/ps2, and after 200ps my velocity (gathered from gmx traj with
> an gmx select input) says that the velocity is stable at around 0.04
> nm/ps. throughout the simulation the velocity slightly increases due
> to the atoms rearranging etc.
>
> Now I want to simulate the same behaviour, but for a longer amount of
> time. I therefore take the exact same MDP file, and change nothing
> except the time-related parameters. I change the number of total steps
> and the timestep, but leave the acceleration intact. After analysing
> the data I get a MUCH higher velocity! I can understand this due to
> rearranging of the atoms on the longer term, but after the same 200ps
> the velocity is also way higher.
>
> So during my smaller run the velocity was 0.04 nm/ps after 200 ps, in
> this longer run, the velocity is 0.2 nm/ps after the same 200ps. How
> is this possible? The exact same acceleration is applied.
>
> Am I missing something?
> --
> Gromacs Users mailing list
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Re: [gmx-users] Regarding extending simulations with change in .mdp file

[Mark Abraham]

Hi,

gmx grompp -f first -o first
gmx mdrun -deffnm first
gmx grompp -f second -o second
gmx mdrun -deffnm second -cpi first

does what I think you should want. You end up with output files named
first.* and second.* which you can concatenate with trjconv or eneconv if
what you plan to do with them will tolerate the change in per-frame spacing
(NB don't assume any tool actually is capable of agreeing with your
intuition here).

It is technically feasible to arrange mdrun to append to the old files from
the new tpr, but you end up with a data curation problem, because you lose
the metadata that these were different stages, even though all you did was
change output frequency.

Mark

On Mon, May 22, 2017 at 5:35 AM Dilip H N  wrote:

> Hello,
>
> I have ran a energy minimization, followed by nvt, followed by md run. My
> md run mdp (ie., md.mdp) has
>
> dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)]
> nstxout = 5000 ; save coordinates every 10.0 ps
> nstvout = 5000 ; save velocities every 10.0 ps
> nstenergy = 5000 ; save energies every 10.0 ps
> nstlog= 5000 ; update log file every 10.0 ps
> nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
>; nstxout-compressed replaces nstxtcout
> This simulation i have ran for 60 ns.
>
> Now i need extend the simulation for another 20ns, but with the change in
> md.mdp file as:-
> dt = 0.001, and nsteps = 2000
> nstxout= 1000 ; save coordinates every 1.0 ps
> nstvout= 1000 ; save velocities every 1.0 ps
> nstenergy = 1000 ; save energies every 1.0 ps
> nstlog = 1000 ; update log file every 1.0 ps
> nstxout-compressed =1000; save compressed coordinates every 1.0 ps;
>;nstxout-compressed replaces
> nstxtcout
> ie., i want the  dt time step of 0.001 and the outputs
> (nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
> the 20ns md run.
>
> And then i need to have a  complete run of total 80ns [(60ns of the 1st
> mdrun  of dt=0.002*3000) + (20ns of the 2nd mdrun of
> dt=0.001*2000)].
>
>
> How can i do this..??
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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[gmx-users] Graphene

[‪Mohammad Roostaie‬ ‪]

Hi,
I simulated the graphene by using this link 
"http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube;. Then, I 
solvated it in water using 'gmx solvate' command. But, when I wanted to add 
ions in the media by using 'gmx grompp' command, I got this error:...ERROR 6383 
[file graphene1110v.top, line 48377]:  No default Proper Dih. types

ERROR 6384 [file graphene1110v.top, line 48378]:  No default Proper Dih. types

ERROR 6385 [file graphene1110v.top, line 48379]:  No default Proper Dih. types
Excluding 3 bonded neighbours molecule type 'graphene'Removing all charge 
groups because cutoff-scheme=Verlet
There was 1 note
---Program gmx grompp, 
VERSION 5.1.4Source code file: 
/home/jemmyhu/work/software/gromacs/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c,
 line: 1738
Fatal error:There were 6385 errors in input file(s)For more information and 
tips for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors
Can you please help me?
Best,Mohammad
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Re: [gmx-users] Need to confirm parameters.

[Sailesh Bataju]

>The easiest thing to do
>(solving this issue and #1) is to create an isobutane .rtp entry and have
>pdb2gmx do all the work for you.  It's very simple to do.

> -Justin

Thank you sir, I've exactly followed your steps. I've created
isobutane.rtp file and modified residuetypes.dat file by adding IBUT
as Protein and then created PDB file from prodrg server. Then using
pdb2gmx command finally got this result:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading prodrg_ibut.pdb...
WARNING: all CONECT records are ignored
Read 14 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 14 atoms

  chain  #res #atoms
  1 ' ' 1 14


WARNING: there were 4 atoms with zero occupancy and 8 atoms with
 occupancy unequal to one (out of 14 atoms). Check your pdb file.

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/isobutane.rtp
Residue 1
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
Processing chain 1 (14 atoms, 1 residues)
Identified residue IBUT0 as a starting terminus.
Identified residue IBUT0 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
No suitable end (N or 5') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
No suitable end (C or 3') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
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...
Warning: Short Bond (5-1 = 0.025 nm)
Warning: Long Bond (5-6 = 0.99084 nm)
Warning: Long Bond (1-2 = 0.944378 nm)
Warning: Long Bond (1-3 = 0.895661 nm)
Warning: Long Bond (1-4 = 0.866986 nm)
Warning: Long Bond (7-8 = 0.502204 nm)
Warning: Long Bond (7-9 = 0.567317 nm)
Warning: Long Bond (7-10 = 0.92202 nm)
Warning: Long Bond (11-12 = 0.592831 nm)
Warning: Long Bond (11-13 = 0.700231 nm)
Warning: Long Bond (11-14 = 0.729592 nm)
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

Writing coordinate file...
- PLEASE NOTE 
You have successfully generated a topology from: prodrg_ibut.pdb.
The Charmm36 force field is used.
- ETON ESAELP 


1. According to the first warning like this "there were 4 atoms with
zero occupancy and 8 atoms with  occupancy unequal to one (out of 14
atoms)"

Is that a kind of error. Did I do any mistake as it said?

2. If i don't add IBUT as Protein in residuetypes.dat file I get error
like this however I get same topol.top file.

"Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (14 atoms, 1 residues)
Warning: Starting residue IBUT0 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

---
Program: gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)

Fatal error:
Residue 'IBUT' not found in residue topology database"

I've no idea whether I've successfully generated those files.

Thank you very much.
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[gmx-users] mdrun failed

[fatemeh ramezani]

 Hi dear gmx-usersI want to simulate gold surface - proteininteraction by 
GOLP-CHARMM forcefield. In md step, after 7 ps , without anyreason mdrun 
failed. md.mdp contains:





title   = gold

cpp = cpp

include =

 

; RUN CONTROL PARAMETERS

integrator  = md

;comm_mode  = Linear

;nstcomm =   1

;comm_grps = Protein  non-Protein

;nstcalcenergy  = 1

; ENERGY MINIMIZATIONOPTIONS

; Force tolerance andinitial step-size

emtol   = 500.0

emstep  = 0.001

tinit   = 0.000

dt  = 0.001

nsteps = 10

 

; OUTPUT CONTROL OPTIONS

nstxout = 3000

nstvout = 3000

nstfout = 0

nstlog  = 1

nstenergy   = 3000

;nsttcouple = 5

; Output frequency andprecision for xtc file

nstxtcout   = 3000

xtc-precision   = 3000

 

 

 

; NEIGHBORSEARCHINGPARAMETERS

; Periodic boundaryconditions: xyz (default), no (vacuum)

pbc = xyz

periodic_molecules  = yes

; nblistcut-off  

rlist   = 1.10

 

; OPTIONS FORELECTROSTATICS AND VDW

; Method for doingelectrostatics

coulombtype = PME

r_coulomb= 1.1

;pme_order   = 6

;fourierspacing   = 0.10

ewald_rtol  = 1e-06

ewald_geometry  = 3d

 

; Method for doing Vander Waals

vdw-type= switch

; cut-offlengths 

rvdw-switch = 0.90

rvdw= 1.10

 

; OPTIONS FORBONDS  

constraints = all-bonds

constraint-algorithm= Lincs

lincs-order = 8

lincs-iter  = 12

; Lincs will write awarning to the stderr if in one step a bond

; rotates over moredegrees than

lincs-warnangle = 90

 

; OPTIONS FOR WEAKCOUPLING ALGORITHMS

; Temperature coupling

Tcoupl  = Nose-Hoover

nhchainlength  = 1

; Groups to coupleseparately

tc-grps =ProteinNon-Protein

; Time constant (ps) andreference temperature (K)

tau-t   = 0.2 0.2

ref-t   = 310 310

 

; Non-equilibrium MDstuff

freezegrps  = slab

freezedim   = Y Y Y

 

Fatemeh Ramezani

 

mdrun command is:

 nohup mdrun -s md.tpr-o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin 
on -pinoffset 1  &

 

the last line of md.log is:

 Step   Time Lambda

   7460    7.46000    0.0

 

   Energies (kJ/mol)

    U-B    Proper Dih. Improper Dih.  CMAP Dih.  LJ-14

    5.39081e+04    1.47221e+04    3.15826e+03   -1.85050e+03    1.80904e+04

 Coulomb-14    LJ (SR)   Coulomb (SR)   Coul. recip.  Potential

    2.97824e+05    2.17254e+12   -6.91585e+06    3.01612e+04    2.17254e+12

    Kinetic En.   Total Energy Conserved En.    TemperaturePressure (bar)

    7.71065e+14    7.73237e+14    9.41950e+16    2.61554e+11    2.41578e+12

   Constr. rmsd

    1.15453e-01

 

The last line of nohup.out is:

 Changing nstlist from10 to 40, rlist from 1.1 to 1.1

 Using 1 MPI thread

Using 3 OpenMP threads

Applying core pinning offset 1

Setting the maximum number of constraint warnings to -1

 

Back Off! I just backed up fws_md3.trr to ./#fws_md3.trr.20#

 Back Off! I justbacked up traj_comp.xtc to ./#traj_comp.xtc.22#

 Back Off! I justbacked up md3.edr to ./#md3.edr.20#

starting mdrun 'Protein in water'

10 steps,    100.0ps.

 

Can you help me to prevent from mdrun failing?

Thank you very much

Fatemeh Ramezani
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[gmx-users] Problem with accelerations

[Kamps, M.]

Dear GMX users,

I have some strange behaviour which I cannot explain.

I want to accelerate atoms through my box at a certain velocity. Since
I can only adjust the acceleration, I have to trial-and-error my way
to the right accelerations.

To do this, I create a smaller 'testing' simulation, which is
continued from an extensive equilibrium. I apply an acceleration of
0.05 nm/ps2, and after 200ps my velocity (gathered from gmx traj with
an gmx select input) says that the velocity is stable at around 0.04
nm/ps. throughout the simulation the velocity slightly increases due
to the atoms rearranging etc.

Now I want to simulate the same behaviour, but for a longer amount of
time. I therefore take the exact same MDP file, and change nothing
except the time-related parameters. I change the number of total steps
and the timestep, but leave the acceleration intact. After analysing
the data I get a MUCH higher velocity! I can understand this due to
rearranging of the atoms on the longer term, but after the same 200ps
the velocity is also way higher.

So during my smaller run the velocity was 0.04 nm/ps after 200 ps, in
this longer run, the velocity is 0.2 nm/ps after the same 200ps. How
is this possible? The exact same acceleration is applied.

Am I missing something?
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[gmx-users] Fw: mdrun failure

[fatemeh ramezani]

 Hi dear gmx-usersIwant to simulate gold surface - protein interaction by 
GOLP-CHARMM forcefield.In md step, after 7 ps , without any reason mdrun 
failed. md.mdp contains: title                   = goldcpp                     
=cppinclude                 =  ;RUN CONTROL PARAMETERSintegrator              = 
md  ;ENERGY MINIMIZATION OPTIONSemtol                   = 500.0emstep           
       = 0.001tinit                   = 0.000dt                      
=0.001nsteps = 10 ;OUTPUT CONTROL OPTIONSnstxout                 = 
3000nstvout                 = 3000nstfout                 = 0nstlog             
     = 1nstenergy               = 3000 ;Output frequency and precision for xtc 
filenstxtcout               = 3000xtc-precision           = 3000 
;NEIGHBORSEARCHING PARAMETERS;Periodic boundary conditions: xyz (default), no 
(vacuum)pbc                     =xyzperiodic_molecules      = yesrlist          
         = 1.10 ;OPTIONS FOR ELECTROSTATICS AND VDW;Method for doing 
electrostaticscoulombtype             = PMEr_coulomb                = 
1.1ewald_rtol              = 1e-06ewald_geometry          = 3d ;Method for 
doing Van der Waalsvdw-type                = switchrvdw-switch             = 
0.90rvdw                    = 1.10 ;OPTIONS FOR BONDS    constraints            
 = h-bondsconstraint-algorithm    = Lincslincs-order             = 8lincs-iter  
            = 12;Lincs will write a warning to the stderr if in one step a 
bond;rotates over more degrees thanlincs-warnangle         = 90 ;OPTIONS FOR 
WEAK COUPLING ALGORITHMS;Temperature coupling  Tcoupl                  = 
Nose-Hoovernhchainlength = 1;Groups to couple separatelytc-grps                 
= Protein  Non-Protein;Time constant (ps) and reference temperature (K)tau-t    
               = 0.2 0.2ref-t                   = 310 310 ;Non-equilibrium MD 
stufffreezegrps              = slabfreezedim               = Y Y Y mdrun 
command is: nohup mdrun -smd.tpr -o md.trr -c md.pdb -g md.log -e md.edr -nt 3 
-dd 1 -pin on -pinoffset 1 & the last line of md.logis: Step          Time      
   Lambda          7460        7.46000       0.0    Energies(kJ/mol)        
   U-B    Proper Dih.  Improper Dih.     CMAP Dih.          LJ-14   5.39081e+04 
   1.47221e+04    3.15826e+03  -1.85050e+03    1.80904e+04    Coulomb-14        
LJ (SR)   Coulomb (SR)  Coul. recip.      Potential   2.97824e+05    
2.17254e+12   -6.91585e+06   3.01612e+04    2.17254e+12    KineticEn.   Total 
Energy  Conserved En.    Temperature Pressure(bar)   7.71065e+14    7.73237e+14 
   9.41950e+16   2.61554e+11    2.41578e+12   Constr.rmsd   1.15453e-01 The 
last line ofnohup.out is:  Changing nstlist from 10to 40, rlist from 1.1 to 1.1 
Using 1 MPI threadUsing 3 OpenMP threadsApplying core pinningoffset 1Setting 
the maximumnumber of constraint warnings to -1 Back Off! I just backedup 
fws_md3.trr to ./#fws_md3.trr.20# Back Off! I just backedup traj_comp.xtc to 
./#traj_comp.xtc.22# Back Off! I just backedup md3.edr to 
./#md3.edr.20#starting mdrun 'Proteinin water'10 steps,   100.0 ps. Can you 
help me toprevent from mdrun failing?Thank you very much 
 Fatemeh Ramezani

   
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Re: [gmx-users] About using GLYCAM force field in Gromacs

[WT Ren]

you can try charmm-gui

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn *

On Tue, May 23, 2017 at 11:20 AM, 维维  wrote:

> Dear Gromacs Users,
>
>   I want to know that if there is a easy way of using GLYCAM force field
> in Gromacs. Thanks in advance!
>
> Best regards
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>
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