[gmx-users] setting up a pull vec

[abhisek Mondal]

Hi,

I'm trying to run a umbrella sampling using following pull code:
; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= JZ4
pull_group2_name= Protein_chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= direction-periodic
pull_coord1_groups  = 1 2
pull_coord1_dim = Y Y Y ; pulling in all dimension
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 500   ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0

This approach needs me to specify a pulling vec which is essentially not
0,0,0.

Could you please suggest me a way to decide how to provide the pull vec ?

Thanks.

-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] Post Permission

[Victor Rosas Garcia]

You just did.

Victor

2016-11-24 14:51 GMT-06:00 Sanim Rahman :

> Hello,
>
> I would like access to post to the mailing list. Thank you!
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Undergraduate Researcher, Global Center for Hearing and Speech Research
> Honors College Engineering Peer Advisor
> 
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[gmx-users] Removal of Waters in Hydrophobic Core

[Sanim Rahman]

Hello,

I am currently working through the second tutorial of the Bevan Labs KALP15
simulation. I am attempting to use the keepbyz.pl script to remove the
waters in the hydrophobic core. I have designated a upperz and
lowerz coordinated and followed the entire section highlighted in the
instructions, however, my output (new_system_sequential_numbers.gro) has no
deleted water molecules. It is the same system as  solvated.gro.

I believe my error is within the keepbyz.pl file, because when I input the
command:

chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro

the file "keep_these_waters.gro" is an empty file.

Here is my script for keepbyz.pl:

#!/bin/bash
# give new_waters.gro as first command line arguement
upperz=5.821
lowerz=0.574
sol=SOL
count=0
cat $1 | grep "$sol" | while read line; do
  for first in $line; do
break
  done
  if [ "$count" = 3 ]; then
count=0
  fi
  count=$(expr $count + 1)
  if [ "$count" != 1 ]; then
continue
  fi
  l=${#line}
  m=$(expr $l - 24)  // would use -48 if velocities are also in .gro and
-24 otherwise
  i=1
  for word in ${line:$m}; do
if [ "$i" = 1 ]; then
  popex=$word
else
  if [ "$i" = 2 ]; then
popey=$word
  else
if [ "$i" = 3 ]; then
  popez=$word
  break
fi
  fi
fi
i=$(expr $i + 1)
  done
  nolx=`echo "$popez > $upperz" | bc`
  nohx=`echo "$popez < $lowerz" | bc`
  myno=$(expr $nolx + $nohx)
  if [ "$myno" != 0 ]; then
z=${#first}
if [ "$z" != 8 ]; then
  sfirst="[[:space:]]$first"
else
  sfirst=$first
fi
`echo grep $sfirst $1`
  fi
done

I will appreciate the help!

Regards,

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Undergraduate Researcher, Global Center for Hearing and Speech Research
Honors College Engineering Peer Advisor

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[gmx-users] Post Permission

[Sanim Rahman]

Hello,

I would like access to post to the mailing list. Thank you!

Regards,

*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Undergraduate Researcher, Global Center for Hearing and Speech Research
Honors College Engineering Peer Advisor

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[gmx-users] grp 1 does not have same number of elements as grp 1

[Poncho Arvayo Zatarain]

Hello: I want to analyze order parameters for a 128 molecules of DPPC/ 128 
moleculesDPPE/Drug membrane, but when i run gmx_order -s npt.tpr -f npt.xtc -n 
sn1.ndx -d z -od deuter_sn1.xvg, the following error appears: grp 1 does not 
have same number of elements as grp 1. I deleted 0-3 (System, DPPC, DPPE, Drug) 
and also 0-4 (System, DPPC, DPPE, Drug and TIP3)) and the error remains. What 
can i do in this case? Thanks
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[gmx-users] Lennard-jones walls

[Lamm Gro]

Dear Gromacs users ,

I am new in Gromacs so maybe my question is so elementary question ! sorry
about that.
I want to use lennard-jones 9-3 walls for confining water between them .
But the problem is I don't know how I can set epsilon and sigma for these
walls !

Can you please give me an example about using walls in Gromacs ?

Regards,
Saeed.
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Re: [gmx-users] Melting temperature for the lipid bilayer

[Piggot T .]

Hi,

I'd suggest it is a combination of 4 and 5. 

It is still not completely clear how you are determining if the membrane is 
classed as liquid disordered or not and also why you think it is too ordered in 
your simulations at 350K (are they in a gel phase or just in a more ordered 
state than you'd expect?). I understand lower APL and higher order parameters 
mean a more ordered membrane, but what are you expecting to see with DSPS above 
the phase transition temperature and why? I'm not aware of experimental 
information regarding these values for DSPS (although that doesn't mean the 
information isn't out there).

That said, it is known that PS doesn't perform particularly well in the 
CHARMM36 force field, even with the re-parameterisation of the ion interactions 
(see http://www.sciencedirect.com/science/article/pii/S0005273616303145) and 
will result in too ordered membranes. Combine this with the fact that you are 
using it within GROMACS (which results in slightly more ordered membranes with 
the CHARMM36 lipids compared to other simulation packages, as referred to in 
the paper you linked to), I'm not surprised that your membranes are more 
ordered than you think they should be.

As for cut-off's, switching off at 8A will help slightly increase disorder in 
your membrane. If you have a membrane only system, I'd definitely go for this. 
I believe the recommendation for using 10A (again in the paper your linked to) 
was to be consistent with other parts of the CHARMM36 force field (e.g. the 
protein parameters). The lipids were originally parameterised with the 8A 
switching.

If you'd like something that is more disordered for DSPS at 350K, I'd choose 
another force field. Slipids would be an easy choice (you should be able to use 
the starting structures you already have) and from some tests of POPS and DOPS 
I've done, it should give you a more disordered membrane. Otherwise, you will 
need to accept the limitations of the force field you have chosen.

Cheers

Tom

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mohsen 
Ramezanpour [ramezanpour.moh...@gmail.com]
Sent: 24 November 2016 03:48
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Melting temperature for the lipid bilayer

Dear Thomas,

Thanks for your comment,
Sorry all as the emails got a bit deviated from the main question.

Problem:
I want to do simulation on a DSPS bilayers with charmm36 ff in
"liquid_disordered" phase.
To do so, I need to find the right temperature that gives me DSPS in
liquid_disordered.
Since the reported experimental T is 341 K, I chose 350 and 355 K but it
did not give a liquid_disordered phase (till 250 ns) in these temperatures.
So, I tried higher T values of 360 and 365.
365 results in the right phase. Since 365 has a gap of 24 with experimental
value I got suspicious about it (probably there is something wrong in my
simulations
but I do not know which part)

So, there are different possibilities:
1) .mdp parameters are not right
Here is a copy of parameters I use for my simulations.

integrator  = md
dt  = 0.002
nsteps  = 15000
nstlog   = 1
nstxout = 50
nstvout = 50
nstfout  = 50
nstcalcenergy = 1000
nstenergy   = 1
;
cutoff-scheme = Verlet
nstlist  = 20
rlist  = 1.2
coulombtype   = pme
rcoulomb = 1.2
vdwtype   = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps   = lipids   WI
tau_t   = 1.01.0
ref_t= 360360
;
pcoupl  = Parrinello-Rahman
pcoupltype   = semiisotropic
tau_p= 5.0
compressibility = 4.5e-5  4.5e-5
ref_p = 1.0 1.0
;
constraints   = h-bonds
constraint_algorithm= LINCS
;
nstcomm   = 100
comm_mode = linear
comm_grps   = lipids  WI
;
refcoord_scaling= com



2) force field parameters (.itp) for DSPS provided by Charmm-GUI are not
right (there is no specific study for DSPS. DSPS is made by PS headgroups
and DS tails)
As I checked, the parameters (at least the charges and bonds) for DS tails
and PS groups are consistent with what is in other lipids including either
PS or DS.
Maybe there are some parts hidden to my eyes and I miss them unconsciously.
I checked bonds as I thought there might be some bonds between two tails by
mistake. That was not the case, though.


3) sampling (250 ns) for each T is not enough to get the right phase.
I am testing this by going to 500 ns. 500 should be fairly en