Re: [gmx-users] error in phosphoserine simulation during MD

[Justin Lemkul]

On 6/17/17 4:05 PM, marzieh dehghan wrote:

Hi

Dear all

I want to simulate a protein containing phosphoserine using MD, so I place
the force field into the working directory and modified all parameters of
force field for example SEP (phosphoserine) was added as Protein in the
residuestypes.dat , but I confronted the following error?

Atom N is used in an interaction of type improper in the topology database,
but an atom of that name was not found in residue number 3.



Can you please provide your exact pdb2gmx command and the full screen output? 
There's a lot of potentially diagnostic information there.  You also may simply 
be missing atoms - not all experimental structures are complete and are clearly 
indicated by MISSING lines in the PDB file.


-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] error in phosphoserine simulation during MD

[marzieh dehghan]

Hi

Dear all

I want to simulate a protein containing phosphoserine using MD, so I place
the force field into the working directory and modified all parameters of
force field for example SEP (phosphoserine) was added as Protein in the
residuestypes.dat , but I confronted the following error?

Atom N is used in an interaction of type improper in the topology database,
but an atom of that name was not found in residue number 3.

please let me know how to solve this problem

best wishes






*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] FLUCTUATION IN DISTANCE

[Justin Lemkul]

On 6/17/17 11:47 AM, Neha Gupta wrote:

Hi gromacs users,

How to examine the fluctuation in distance in protein ligand binding,
between protein residue and the ligand?

What is the exact command ?



Read about how to use gmx distance.  Then perform statistical analysis on the 
time series.


-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 create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation

[Justin Lemkul]

On 6/17/17 8:55 AM, Sajeewa Pemasinghe wrote:

Hi all,

I have to carry out MD simulations involving PEG 6000 molecules. When I
first build this it is a very long (~480 Angstrom) linear chain. I have the
bond/angle/dihedral parameters for this linear structure. Usually when I
introduce a non-standard residue, I perform an optimization in Gaussian and
then get the parameters and create an itp file with those parameters. In
this case as the molecule is too big I cannot go for a quantum
optimization.

1) Should I put this in a box of water and let it equilibrate and get the
parameters for the equilibrated structure? But that box would then be huge
at the beginning because at the beginning the structure is linear(Is there
a way out of this?).  This must be quite a naive question. But could you
give me your suggestions as  to what path I should follow?

2) I came across this link .
http://www.gromacs.org/Documentation/How-tos/Polymers

So should I create separate rtp files for the above three fragments? Or
should I go with creating an itp file and include that string in the .top
file?



A polymer is just a chain of repeating units.  You should not attempt to 
optimize/parametrize an entire polymer, because you will get 
conformation-specific parameters that are likely to be unphysical.  If 
parameters do not already exist (I find it unlikely that nobody has simulated 
PEG before), you can easily parametrize the ethylene glycol units by optimizing 
monomers and dimers to get charges and bonded parameters.


-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] FLUCTUATION IN DISTANCE

[Neha Gupta]

Hi gromacs users,

How to examine the fluctuation in distance in protein ligand binding,
between protein residue and the ligand?

What is the exact command ?

Thanks,
Neha
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Re: [gmx-users] using groups in index for gmx select

[Mark Abraham]

Hi,

I don't know, but like all kinds of complex things, start with a simple
thing and add complexity. Can you get the input index group to be the
output group?

Mark

On Wed, 14 Jun 2017 07:45 Sahithya S Iyer  wrote:

> Hi gmx users,
>
> Can anyone please tell me how to use a group in index file in gmx select.
> For example -
>
> *gmx select -n index.ndx -select 'name "OH2" and within 2 of com of name "P
> and r 1-36"' -on P-water.ndx -s step7_production.tpr*
>
> does not write out anything in the index (P-water.ndx) file. I have defined
> this group in the index file. Can I use this in the -select command? If so,
> how ?
>
>  Basically I would like to select oxygen atoms of water molecules that are
> 2 nm around the phosphate groups of one monolayer.
>
> Any help is much appreciated.
> Thanks in advance.
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Re: [gmx-users] using groups in index for gmx select

[Nikhil Maroli]

Hi,

>Basically I would like to select oxygen atoms of water molecules that are
>2 nm around the phosphate groups of one monolayer.


There is Tcl script available in NAMD for selecting the oxygen atoms
of water molecules that are XX nm around XXX. Sorry, I don't have the
link, but you can easily get it from the google search. Radial
distribution function might give some information about these, and you
can make a rough calculation out of that.
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[gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation

[Sajeewa Pemasinghe]

Hi all,

I have to carry out MD simulations involving PEG 6000 molecules. When I
first build this it is a very long (~480 Angstrom) linear chain. I have the
bond/angle/dihedral parameters for this linear structure. Usually when I
introduce a non-standard residue, I perform an optimization in Gaussian and
then get the parameters and create an itp file with those parameters. In
this case as the molecule is too big I cannot go for a quantum
optimization.

1) Should I put this in a box of water and let it equilibrate and get the
parameters for the equilibrated structure? But that box would then be huge
at the beginning because at the beginning the structure is linear(Is there
a way out of this?).  This must be quite a naive question. But could you
give me your suggestions as  to what path I should follow?

2) I came across this link .
http://www.gromacs.org/Documentation/How-tos/Polymers

So should I create separate rtp files for the above three fragments? Or
should I go with creating an itp file and include that string in the .top
file?

I really appreciate your help on this.

Thank you

Sajeewa
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Re: [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)

[Justin Lemkul]

On 6/17/17 2:23 AM, Apramita Chand wrote:

Dear Justin,
The normal (non-annealing) equilibration works fine. 100ps of NVT and it
easily reaches 300K. There are no error messages.
Am I doing the simulated annealing correctly?



Looks fine, other than generating velocities at 300 K but specifying 0 K as the 
initial temperature for annealing.  If you're just equilibrating a system, I 
think annealing is a waste of time.


-Justin


yours sincerely
Apramita

Message: 4
Date: Fri, 16 Jun 2017 13:21:18 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] System reaches ~124K after simulated
 annealing upto 300K
Message-ID: <8fe97070-c577-de07-ba25-64a7230f6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/16/17 10:38 AM, Apramita Chand wrote:

Dear All,
I have used the following nvt.mdp file to gradually warm my system upto
300K but just reach upto 124K. I have used variety of options in the
simulated annealing like taking less no. of time intervals but in vain
Then, I have to perform manually the gradual heating process which takes

me

to 300K
Why doesn't this work?



Anything that goes that haywire is simply unstable.  De-complicate your
life and
try to do a normal (non-annealing) MD and see if it works.  If not, then
diagnose further.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_
Unstable_System

-Justin


Yours sincerely,
Apramita



   VARIOUS PREPROCESSING OPTIONS
define   = -DPOSRES
; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002 ; time step (in ps)
nsteps   = 5 ; number of steps
; OUTPUT CONTROL OPTIONS
nstxout = 500   ; save coordinates every ps
nstvout = 500   ; save velocities every ps
nstenergy   = 500   ; save energies every ps
nstlog  = 500   ; update log file every ps
energygrps  = Protein SOL
; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME  ; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing   = 0.16 ; grid spacing for FFT
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
5
tcoupl   = v-rescale; Couple temperature to
external heat bath according to velocity re-scale method
tc-grps  =  Protein  SOL ; Use separate heat baths for
Protein and Non-Protein groups
tau_t= 0.10.1; Coupling time constant,
controlling strength of coupling
ref_t= 300300; Temperature of heat bath
; Dispersion correction
DispCorr = EnerPres ; account for vdw cut-off
; Pressure coupling is off
pcoupl  = no; no pressure coupling in
NVT
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes; Assign velocities to particles by
taking
them randomly from a Maxwell distribution
Different numbers give different sets of velocities
gen_temp = 300; Temperature to generate corresponding
Maxwell distribution
gen_seed = -1 ; Seed for (semi) random number
generation.
; OPTIONS FOR BONDS
constraints  = all-bonds ; All bonds will be treated as
constraints (fixed length)
continuation = no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
lincs_iter   = 1; accuracy of LINCS
lincs_order  = 4; also related to accuracy
; Simulated Annealing
annealing= single single
annealing_npoints= 4 4
annealing_time= 0 50 75 100 0 50 75 100
annealing_temp= 0 100 200 300 0 100 200 300



--
==

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] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)

[Apramita Chand]

Dear Justin,
The normal (non-annealing) equilibration works fine. 100ps of NVT and it
easily reaches 300K. There are no error messages.
Am I doing the simulated annealing correctly?

yours sincerely
Apramita

Message: 4
Date: Fri, 16 Jun 2017 13:21:18 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] System reaches ~124K after simulated
annealing upto 300K
Message-ID: <8fe97070-c577-de07-ba25-64a7230f6...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/16/17 10:38 AM, Apramita Chand wrote:
> Dear All,
> I have used the following nvt.mdp file to gradually warm my system upto
> 300K but just reach upto 124K. I have used variety of options in the
> simulated annealing like taking less no. of time intervals but in vain
> Then, I have to perform manually the gradual heating process which takes
me
> to 300K
> Why doesn't this work?
>

Anything that goes that haywire is simply unstable.  De-complicate your
life and
try to do a normal (non-annealing) MD and see if it works.  If not, then
diagnose further.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_
Unstable_System

-Justin

> Yours sincerely,
> Apramita
>
>
>
>   VARIOUS PREPROCESSING OPTIONS
> define   = -DPOSRES
> ; RUN CONTROL PARAMETERS
> integrator   = md
> dt   = 0.002 ; time step (in ps)
> nsteps   = 5 ; number of steps
> ; OUTPUT CONTROL OPTIONS
> nstxout = 500   ; save coordinates every ps
> nstvout = 500   ; save velocities every ps
> nstenergy   = 500   ; save energies every ps
> nstlog  = 500   ; update log file every ps
> energygrps  = Protein SOL
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 0.9
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = PME  ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing   = 0.16 ; grid spacing for FFT
> rcoulomb = 0.9
> vdw-type = Cut-off
> rvdw = 1.4
> ; Temperature coupling
> 5
> tcoupl   = v-rescale; Couple temperature to
> external heat bath according to velocity re-scale method
> tc-grps  =  Protein  SOL ; Use separate heat baths for
> Protein and Non-Protein groups
> tau_t= 0.10.1; Coupling time constant,
> controlling strength of coupling
> ref_t= 300300; Temperature of heat bath
> ; Dispersion correction
> DispCorr = EnerPres ; account for vdw cut-off
> ; Pressure coupling is off
> pcoupl  = no; no pressure coupling in
> NVT
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel  = yes; Assign velocities to particles by
> taking
> them randomly from a Maxwell distribution
> Different numbers give different sets of velocities
> gen_temp = 300; Temperature to generate corresponding
> Maxwell distribution
> gen_seed = -1 ; Seed for (semi) random number
> generation.
> ; OPTIONS FOR BONDS
> constraints  = all-bonds ; All bonds will be treated as
> constraints (fixed length)
> continuation = no   ; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> lincs_iter   = 1; accuracy of LINCS
> lincs_order  = 4; also related to accuracy
> ; Simulated Annealing
> annealing= single single
> annealing_npoints= 4 4
> annealing_time= 0 50 75 100 0 50 75 100
> annealing_temp= 0 100 200 300 0 100 200 300
>

--
==

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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