# AW: First meeting with NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jun 10 2013 - 00:35:06 CDT

Hi James,

you know that you can set the box dimensions before solvating? Additionally, you may not set a PBC box smaller, than the atoms are already placed, because the simulation will crash due the atom being initially wrapped into each other. Furthermore, as it is a PBC box, it doesn’t matter if your box is centered or not. Think about it.

Norman Geist.

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von James Starlight
Gesendet: Freitag, 7. Juni 2013 07:14
An: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: First meeting with NAMD

One extra question-

definition of the PBC vectors

assuming that I have system protein in water, visualization in VMD give me the next min max and initial center coordinates of my solvated system

vmd > measure minmax \$everyone
{2.0339999198913574 44.51599884033203 -6.256999969482422} {62.07699966430664 116.66600036621094 62.32600021362305}
vmd > measure center \$everyone
32.14433288574219 80.72885131835938 27.922433853149414
vmd >

than I've defining rectangular box with vectors

cellBasisVector1 60.0 0.0 0.0
cellBasisVector2 0.0 60.0 0.0
cellBasisVector3 0.0 0.0 60.0
cellOrigin 30.0 30.0 30.0

In that case I dont need big value on Y (possible max up to 116 ). AS the result If I vary cell origin in Y from 0 to 60 my system will placed outside of PBC. With center on the y = 30 protein placed on bottom of the box. But how I can place in the middle of box on y dimension (I have no problem with X and Z in the same box) fixed y up to 60 ? (If I increade it up to maximun my protein will be placed correctly but I've obtain very big box.

James

2013/6/6 Norman Geist <norman.geist_at_uni-greifswald.de>

Hi James,

Do you mean you did the whole equilibration while restraining positions of all atoms of the protein? If so, please think about what a minimization and equilibration is meant for. The error you see means, that in the moment where the restrains are removed, high forces were unloading which blows apart you system. This is of course due not allowing the protein to remove these tensions while the minimization and equilibration steps. You should at least free the protein during minimization. If you need to restrain anything, try to do it relative here not absolute (position), check out the “extrabonds” command.

If I got you wrong, please explain more detailed what exactly you did.

Norman Geist.

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von James Starlight

Gesendet: Mittwoch, 5. Juni 2013 12:22
An: namd-l_at_ks.uiuc.edu

Betreff: Re: namd-l: First meeting with NAMD

Today I've tried to perform small simulation of the water-soluble protein (gfp with embedded chromophore).

After minimisation + nvt+ nvp equilibration with applied position restraines to all protein atom my simulation was crushed during begining of the production run with the eror

LDB: =============== DONE WITH MIGRATION ================ 57.1231
Info: Benchmark time: 4 CPUs 0.055768 s/step 0.322732 days/ns 108.641 MB memory
ERROR: Constraint failure in RATTLE algorithm for atom 938!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

WallClock: 57.500668 CPUTime: 57.500668 Memory: 108.890625 MB
Program finished.

According to the error 938 atom correspond to the N-term of the residue connected to the chromophore of my GFP which I've included to the rest of backbone by means of psfgen.

Also I've observed behavior of my system during minimisation and equilibration and didnt observe any significant artifacts (the geometry of the chromophore and connected to it residues was correct).

Below you can see my parameters of simulation.

structure ionized.psf
coordinates ionized.pdb
outputName md
bincoordinates npt.restart.coor
binvelocities npt.restart.vel
extendedSystem npt.restart.xsc

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
parameters FP.prm

cellBasisVector1 62.0 0. 0.0
cellBasisVector2 0.0 80.0 0.0
cellBasisVector3 0.0 0 62.0
cellOrigin 31.0 40.0 31.0

wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 2 ;# damping coefficient (gamma) of 5/ps
langevinTemp 310
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.0
langevinPistonDecay 500.0
langevinPistonTemp 310

Does it contain any errors assuming that I'm simulating water soluble protein in NPT conditions?

2) Could you provide me with the example of the input file for psfgen for automate hydrogen addition according to the existing protonation state ? I've tried to save my structure from VMD (according to the tutorial) but the hydrogens havent been added in that case

Thanks for any suggestions,

James

2013/6/4 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

also I found that conf file should lack for barostat parameters ( simulation in NVT with weak coupling), shouldn't it ? Where I can read about NAMD equilibration protocols?

The NAMD manual!

2) I have some problems with atom names (primarily with names of hydrogens) when I use charm36 (no problems with charm27) assuming that I add hydrogens by means of pdb2pqr where protonation state assigned with the charmm force field

Use psfgen to add the hydrogens again.

James

2013/6/4 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

Hello James, atom selections in VMD are your best friend here. First create a selection (VMD documentation is awesome for this) then:

1) use the measure minmax command

2) set the PDB occupancy for each atom to the force constant

About the force field: why do you assume that charmm36, just because it's newer, doesn't contain the previous charmm27 parameters?

G.

On Tue, Jun 4, 2013 at 10:33 AM, James Starlight <jmsstarlight_at_gmail.com> wrote:

Dear colleagues!

I've examined carefully basic NAMD tutorial (simulation of ubiquiteen) and briefly examined more advanced tutorials. Unfortunately I could not find answers on the questions

1) How quickly PBC vectors could be defined based on the dimensions of my system? (e.g I can define on each vector manually in VMD and show it by means of pbc box but I'm looking in more quick way to define box dimensions automatically and then add it to the conf file).

2) Is there any automatic tools for generation of the position restraints on the specific column in the pdb file ?
I'll be thankful if you show me tutorial where both of that aspects as well as basic of the equilibration in namd was described.

also I'm looking for the charm27 (prm and imp files) parameters with CMAP correcrions where parameters for lipids protein and waters-ions have been present. On the MacKerel webpage I found only newest charm36 params

James

2013/6/4 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>

Did you go through all the wonderful tutorials <http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html> on NAMD? The answers to both questions are there.

On 4 June 2013 15:25, James Starlight <jmsstarlight_at_gmail.com> wrote:

Also some methodological questions

1- How I could properly define PBC vectors based on the input pdb ? ( for comparison gromacs gro format contain box vectors on the last string of the structure file ) Is there some VMD plugin to define pbc automatically ?

2- Defining constraints on the conf file

#constraints
constraints on
consref ???
conskfile ???
conskcol X

its important to define atoms on which that constraints will be included (??? in the above script where it correspond to the only protein atom) How it could be done?

James

2013/6/4 James Starlight <jmsstarlight_at_gmail.com>

Hi Norman!

Thanks for suggestions again. Could you also help with the psfgen (Above I've described my problem)

Here script that I used

package require psfgen
resetpsf
topology top_crq_final.inp

topology top_all36_prot.rtf
pdbalias residue HIS HSE
segment A {

pdb prot_charm1.pdb
first Nter
last NONE
}
coordpdb prot_charm1.pdb A

segment B {
first NONE
last Cter
pdb prot_charm2.pdb

}
coordpdb prot_charm2.pdb B

segment C {
pdb crq.pdb
first NONE
last NONE
}
coordpdb crq.pdb C

guesscoord

writepsf dhp-output.psf
writepdb dhp-output.pdb

Here link correspond to the imaginary connection which I've found in the charm36 params

! 1 refers to previous (N terminal)
! 2 refers to next (C terminal)
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C 2N
!the need for the explicit specification of angles and dihedrals in
!patches linking images has not been tested
!ANGLE 1C 2N 2CA 1CA 1C 2N
!ANGLE 1O 1C 2N 1C 2N 2HN
!DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
!DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
!DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
!DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000

This produces reasonable geometry of chromophore embedded into the rest of the GFP barell but As I understood from the description I should provide some extra parameters for dihedrals and impropers for that connector regions. Assuming that chromophore is the part of the rest of backbone and standart parameters could be used from the backbone aminoacids how I could specifi it for that case ?

Thanks for help,

James

2013/6/4 James Starlight <jmsstarlight_at_gmail.com>

Hi Norman!

Thanks for suggestions again. Could you also help with the psfgen (Above I've described my problem)

Here script that I used

package require psfgen
resetpsf
topology top_crq_final.inp

topology top_all36_prot.rtf
pdbalias residue HIS HSE
segment A {

pdb prot_charm1.pdb
first Nter
last NONE
}
coordpdb prot_charm1.pdb A

segment B {
first NONE
last Cter
pdb prot_charm2.pdb

}
coordpdb prot_charm2.pdb B

segment C {
pdb crq.pdb
first NONE
last NONE
}
coordpdb crq.pdb C

guesscoord

writepsf dhp-output.psf
writepdb dhp-output.pdb

Here link correspond to the imaginary connection which I've found in the charm36 params

! 1 refers to previous (N terminal)
! 2 refers to next (C terminal)
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C 2N
!the need for the explicit specification of angles and dihedrals in
!patches linking images has not been tested
!ANGLE 1C 2N 2CA 1CA 1C 2N
!ANGLE 1O 1C 2N 1C 2N 2HN
!DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
!DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
!DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
!DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000

This produces reasonable geometry of chromophore embedded into the rest of the GFP barell but As I understood from the description I should provide some extra parameters for dihedrals and impropers for that connector regions. Assuming that chromophore is the part of the rest of backbone and standart parameters could be used from the backbone aminoacids how I could specifi it for that case ?

Thanks for help,

James

2013/6/4 Norman Geist <norman.geist_at_uni-greifswald.de>

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von James Starlight
Gesendet: Montag, 3. Juni 2013 16:09
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: First meeting with NAMD

Dear NAMD users!

Hi james,

Recently I've tried to launch my first simulation on NAMD :) (previously I've used Gromacs ).

My questions:

1) Typical gromacs simulation consist of energy minimization + equilibration in NPT ensemble (with position restraints applied on each atoms of protein) + production run.

As I understood minimization should explicitly defined in the conf file

# Minimization
minimize 100
reinitvels \$temperature

run 5000000

but what about equilibration stage ?

How I can perform short simulation with the applied porses prior to the production run?

We usually have the following simulation protocol:

1. Minimization for some thousand steps, depending on system size (check if TOTAL energy converges)

2. Heating up using Langevin thermostat (there are multiple methods and thermostats available)

3. Constant Pressure (remove vacuum bubbles from solvent using piston barostat, also other choices available)

4. Heat again as pressure could have changed anything

5. Free simulation <- production run

Each of these steps is represented by a own namd script. Additionally, each step uses the final coordinates and velocities from the step before, except minimization which start from the initial structure of course.

2) How I can monitor total performance of the GPU utilized in the simulation assuming that I use CUDA.

Depending on what kind of GPU you got, you can try nvidia-smi to check for the utilization (I guess only for Tesla). But as others already said, you should use the CPU:GPU ratio and configuration, that comes with the smallest time/step. Additionally, for most system sizes I got a nice almost two-fold speedup by using “twoawayx yes” in my namd script, you should try the difference. To be sure to get the best performance, it’s worth it to do some benchmarks.

3) I have parameters ( prm and inp files) for some non-standard residue ( GFP chromophore). for this protein I'd like to make model (including protein covalently bonded to the chromophore and solvent) and perform simulation.

Could you provide me with the example or short tutorial for such task?

See VMD and psfgen. Additionally search for the NAMD Tutorial on the net, which is a really nice for starting for both NAMD and VMD.

Thanks for help,

James

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