[gmx-users] unable to understand dPCA

[Seera Suryanarayana]

Dear gromacs users,

I have done simulations of 20 residues length peptide for 300ns. As I would
like to do explore the conformational space I have chosen the dPCA to find
flexible regions. I have gone through the dPCA tutorial from gromacs site
and followed it. First I have generated the index file by mk_angndk and I
got following index file and I have chosen zero group (top one).

[ Phi=180.0_2_43.93 ]
 52523242747454649696768
7188868790999798   101   121   119   120
   123   131   129   130   133   143   141   142   135   139   138   140
   145   162   160   161   164   169   167   168   171   179   177   178
   180   193   191   192   195   204   202   203   206   211   209   210
   213   231   229   230   233   253   251   252   255   270   268   269
   272   286   284   285   288   297   295   296   299   313   312   314

[ Phi=180.0_2_4.18 ]
232725264549474867716970
8690888997   10199   100   119   123   121   122
   129   133   131   132   141   145   143   144   160   164   162   163
   167   171   169   170   177   180   179   188   191   195   193   194
   202   206   204   205   209   213   211   212   229   233   231   232
   251   255   253   254   264   262   266   267   268   272   270   271
   284   288   286   287   295   299   297   298   308   306   310   311

[ Phi=180.0_2_4.60 ]
   215   218   221   219   218   223   219   220   218   225   221   222
   219   227   223   224   221   227   225   226   223   225   227   228
   257   260   262   261   260   266   262   263   261   266   264   265
   301   304   306   305   304   310   306   307   305   310   308   309

Then I have to get another index file which tells to the trjconv to
generate .gro file. Here I am unable to generate index file. As I want
create complete complete peptide .gro file except both terminal residues.
Based on the 2*N/3 formula, it is not possible to create complete .gro
file. Kindly tell how to create complete gro file for peptide of my
interest.

Thanks in advance
Surya
Graduate student
India.
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[gmx-users] paralllelized gromacs run creating same file in many times -reg

[venkat]

Hello,
 I installed Gromacs-2016.4 using (compiled using:
intel-parallel-studio-2016, gcc4.8.5),
I tried gromacs run parallelized on 32 cores, i seen  multiple instances of
mdrun, each one using one MPI process,
also many gromacs header in the log file, in directory  log, ene, traj_comp
files are creating multiple times

so, I expecting your suggestions to rectify this issue.

thank you

*FOR JOB SUBMISSION FOLLOWED SCRIPT USED *
#! /bin/bash
##PBS -l walltime=48:00:00
#PBS -N gromacs
#PBS -q workq
#PBS -l select=2:ncpus=16:mpiprocs=16
#PBS -S /bin/csh
#PBS -V
# Go to the directory from which you submitted the job

cd $PBS_O_WORKDIR

module purge
module load gcc4.8.5
module load gsl-2.0
module load intel-parallel-studio-2016
module load gromacs-2016.4_Plumbedpatch
module load openmpi-3.0
module load plumed-2.4

export MPI_DEBUG=all
export MPI_IB_RAILS=2
export MPI_DSM_DISTRIBUTE=1
export MPI_VERBOSE=1
export MPI_BUFS_THRESHOLD=1
export MPI_BUFS_PER_PROC=1024
export OMP_NUM_THREADS=1

mpirun -np 32 /app/gromacs-2016.4_plumbSWpatch/bin/gmx_mpi mdrun -v -s
topol -nsteps 500 &> 6ter.log


*##DIRECTORY  *
*ls -lrt *

  Feb  1 10:52 #ener.edr.51#
Feb  1 10:52 #ener.edr.50#
Feb  1 10:52 #ener.edr.49#
Feb  1 10:52 #ener.edr.48#
Feb  1 10:52 #ener.edr.47#
Feb  1 10:52 #ener.edr.46#
Feb  1 10:52 #ener.edr.45#
Feb  1 10:52 #ener.edr.44#
Feb  1 10:52 #ener.edr.43#
Feb  1 10:52 #ener.edr.42#
Feb  1 10:52 #ener.edr.41#
Feb  1 10:52 #ener.edr.40#
Feb  1 10:52 #ener.edr.39#
Feb  1 10:52 #ener.edr.38#
Feb  1 10:52 #ener.edr.37#
Feb  1 10:52 #ener.edr.36#
Feb  1 10:52 #ener.edr.35#
Feb  1 10:52 #ener.edr.34#
Feb  1 10:52 #ener.edr.33#
Feb  1 10:52 #ener.edr.32#
Feb  1 10:52 ener.edr
Feb  1 10:52 #traj_comp.xtc.57#
Feb  1 10:52 #traj_comp.xtc.56#
Feb  1 10:52 #traj_comp.xtc.55#
Feb  1 10:52 #traj_comp.xtc.54#
Feb  1 10:52 #traj_comp.xtc.53#
Feb  1 10:52 #traj_comp.xtc.52#
Feb  1 10:52 #traj_comp.xtc.51#
Feb  1 10:52 #traj_comp.xtc.50#
Feb  1 10:52 #traj_comp.xtc.49#
Feb  1 10:52 #traj_comp.xtc.48#
Feb  1 10:52 #traj_comp.xtc.47#
Feb  1 10:52 #traj_comp.xtc.46#
Feb  1 10:52 #traj_comp.xtc.45#
Feb  1 10:52 #traj_comp.xtc.44#
Feb  1 10:52 #traj_comp.xtc.43#
Feb  1 10:52 #traj_comp.xtc.42#
Feb  1 10:52 #traj_comp.xtc.41#
Feb  1 10:52 #traj_comp.xtc.40#
Feb  1 10:52 #traj_comp.xtc.39#
Feb  1 10:52 traj_comp.xtc
Feb  1 10:52 #md.log.70#
Feb  1 10:52 #md.log.69#
Feb  1 10:52 #md.log.68#
Feb  1 10:52 #md.log.67#
Feb  1 10:52 #md.log.66#
Feb  1 10:52 #md.log.65#
Feb  1 10:52 #md.log.64#
Feb  1 10:52 #md.log.63#
Feb  1 10:52 #md.log.62#
Feb  1 10:52 #md.log.61#
Feb  1 10:52 #md.log.60#
Feb  1 10:52 #md.log.59#
Feb  1 10:52 #md.log.58#
Feb  1 10:52 #md.log.57#
Feb  1 10:52 #md.log.56#
Feb  1 10:52 #md.log.55#
Feb  1 10:52 #md.log.54#
Feb  1 10:52 md.log
Feb  1 10:52 6ter.log

*KINDLY GET LOG FROM ATTACHMENT*
​
 6ter.log

​
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Re: [gmx-users] gmx distance

[Justin Lemkul]

On 1/31/18 12:41 PM, Nick Johans wrote:

Sorry, i think there is sth, maybe i've learnt wrong. let me draw it ;)
  | = ZnS SHEET and@=Protein

conf0.gro

|
|
|<(Z)distance=1.76--->@
  t=0
|
|

next time if dZ=0.5 so;
|
|
|<-(Z)distance=1.26>@
  t=t1
|
|

next time if dZ=0.8 so;
|
|
|<-(Z)distance=0.96>@
  t=t2
|
|

I want to tell you this is my last conf.gro

|
|
|
|
|@  t=tn

so WHY it shows me 1.611?how can i proof and calculate this distance?ok
they are not coincident because i have sheet(which interact by it's
surface) and Protein, but why it should be important? because the sheet is
freez and immobile and i just want Z distance. and this distance should be
the absolute distance between 2 point( difference between z=4.287and COM of
protein in each frame). this is all my imagination. What i have
misunderstand?


You're applying a restraint only along z. The protein is free to move in 
x and y, and it has done just that. The total COM distance is produced 
by gmx distance, but again, the z-component of this vector is in 
agreement with what is in pullx.xvg, which is dZ, e.g. the z-component 
of the distance. This is the only quantity that matters.


-Justin


best regards



On Wed, Jan 31, 2018 at 8:17 PM, Justin Lemkul  wrote:



On 1/31/18 11:22 AM, rose rahmani wrote:


Hi,
This is md_pull.mdp

integrator   = md
dt   = 0.001
nsteps   = 400
nstxout  = 1000
nstvout  = 1000
nstfout  = 500
nstlog   = 500
nstenergy= 500
nstxtcout= 500
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = distance
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
---
pullx.xvg;

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.  4.287   1.76284
0.0500  4.287   1.75329
0.1000  4.287   1.74622
0.1500  4.287   1.73983
0.2000  4.287   1.73664
0.2500  4.287   1.7377
.
.

3999.7500   4.287   0.258632
3999.8000   4.287   0.258738
3999.8500   4.287   0.258955
3999.9000   4.287   0.260093
3999.9500   4.287   0.25843
4000.   4.287   0.258025
-
Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
whole
Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg

this is distwhole.xvg
 0.0001.76307740.0185155   -0.0197599   -1.7628694
 0.5001.7529889   -0.01330900.0135729   -1.7528858
 1.0001.7453604   -0.03446920.0751038   -1.7434030
 1.5001.7691813   -0.06215670.0087628   -1.7680674
.
.
3997.5001.61200060.9964043   -1.2400901   -0.2605782
3998.0001.61228910.9971979   -1.2404475   -0.2576084
3998.5001.61245740.9966092   -1.2406733   -0.2598433
3999.0001.61155650.9968075   -1.2396555   -0.2583475
3999.5001.61206160.9964568   -1.2404943   -0.2588253
4000.0001.61162940.9952377   -1.2410750   -0.2580390

as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
group (Protein and ZnS sheet) in last frame are too close to each other.
so
why i see 1.611 in distwhole.xvg?

and could you please tell me what is the relevance of pullx.xvg to g_dist
output?as you see pullx.xvg ensure that distance between 2 group is
decreasing, so...?

is there anything i did not consider?


Your output is completely consistent. You're applying a biasing potential
along the z-dimension only, so that's the only distance that mdrun c

Re: [gmx-users] gmx distance

[Nick Johans]

Sorry, i think there is sth, maybe i've learnt wrong. let me draw it ;)
 | = ZnS SHEET and@=Protein

conf0.gro

|
|
|<(Z)distance=1.76--->@
 t=0
|
|

next time if dZ=0.5 so;
|
|
|<-(Z)distance=1.26>@
 t=t1
|
|

next time if dZ=0.8 so;
|
|
|<-(Z)distance=0.96>@
 t=t2
|
|

I want to tell you this is my last conf.gro

|
|
|
|
|@  t=tn

so WHY it shows me 1.611?how can i proof and calculate this distance?ok
they are not coincident because i have sheet(which interact by it's
surface) and Protein, but why it should be important? because the sheet is
freez and immobile and i just want Z distance. and this distance should be
the absolute distance between 2 point( difference between z=4.287and COM of
protein in each frame). this is all my imagination. What i have
misunderstand?

best regards



On Wed, Jan 31, 2018 at 8:17 PM, Justin Lemkul  wrote:

>
>
> On 1/31/18 11:22 AM, rose rahmani wrote:
>
>> Hi,
>> This is md_pull.mdp
>>
>> integrator   = md
>> dt   = 0.001
>> nsteps   = 400
>> nstxout  = 1000
>> nstvout  = 1000
>> nstfout  = 500
>> nstlog   = 500
>> nstenergy= 500
>> nstxtcout= 500
>> nstlist  = 10
>> rlist= 1.5
>> coulombtype  = pme
>> rcoulomb = 1.5
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> rvdw = 1.2
>> pcoupl   = no
>> gen_vel  = no
>> constraints  = h-bonds
>> ns_type  = grid
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrp-excl   = WAL WAL ZnS ZnS
>> energygrps   = SOL WAL ZnS Protein NA CL
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>>
>> ; Pull code
>> pull= umbrella
>> pull_ngroups= 1
>> pull_group0 = ZnS
>> pull_group1 = Protein
>> pull_geometry   = distance
>> pull_dim= N N Y
>> pull_rate1  = -0.01
>> pull_k1 = 5000
>> pull_start  = yes
>> pull_nstxout= 50
>> ---
>> pullx.xvg;
>>
>> @title "Pull COM"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Position (nm)"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "0 Z"
>> @ s1 legend "1 dZ"
>> 0.  4.287   1.76284
>> 0.0500  4.287   1.75329
>> 0.1000  4.287   1.74622
>> 0.1500  4.287   1.73983
>> 0.2000  4.287   1.73664
>> 0.2500  4.287   1.7377
>> .
>> .
>>
>> 3999.7500   4.287   0.258632
>> 3999.8000   4.287   0.258738
>> 3999.8500   4.287   0.258955
>> 3999.9000   4.287   0.260093
>> 3999.9500   4.287   0.25843
>> 4000.   4.287   0.258025
>> -
>> Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
>> whole
>> Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg
>>
>> this is distwhole.xvg
>> 0.0001.76307740.0185155   -0.0197599   -1.7628694
>> 0.5001.7529889   -0.01330900.0135729   -1.7528858
>> 1.0001.7453604   -0.03446920.0751038   -1.7434030
>> 1.5001.7691813   -0.06215670.0087628   -1.7680674
>> .
>> .
>> 3997.5001.61200060.9964043   -1.2400901   -0.2605782
>> 3998.0001.61228910.9971979   -1.2404475   -0.2576084
>> 3998.5001.61245740.9966092   -1.2406733   -0.2598433
>> 3999.0001.61155650.9968075   -1.2396555   -0.2583475
>> 3999.5001.61206160.9964568   -1.2404943   -0.2588253
>> 4000.0001.61162940.9952377   -1.2410750   -0.2580390
>>
>> as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
>> group (Protein and ZnS sheet) in last frame are too close to each other.
>> so
>> why i see 1.611 in distwhole.xvg?
>>
>> and could you please tell me what is the relevance of pullx.xvg to g_dist
>> output?as you see pullx.xvg ensure that distance between 2 group is
>> decreasing, so...?
>>
>> is there anything i did not consider?
>>
>
> Your output is completely consistent. You're applying a biasing potential
> along the z-dimension only, so that's the only distance that mdrun cares
> about in establishing the reaction coordinate. The pullx.xvg file 

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/30/18 7:00 PM, negar habibzadeh wrote:

hi. in my dopc.gro file i have 128 dopc ,5120 water (sol) with box size of
6.5   6.5   7.5 .i increase z direction from 7.5 nm  to 10 nm ,how can i
add some extra water more than 5120 ??


Just run gmx solvate again.

-Justin


On Mon, Jan 29, 2018 at 5:41 PM, Justin Lemkul  wrote:



On 1/28/18 3:22 PM, negar habibzadeh wrote:


my peptide is a cpp (cell penetrating peptide) . i am going to simulation
this peptide in dopc bilayer , i did lots of methods to build the system
but in nvt step i saw water inside dopc (i used posre for water but when i
removed it to run npt or md ,my problem was not solved ).Is it true that
my
peptide causes water to enter into the membrane because it is a cpp???


Water leaking in immediately at the end of equilibration is almost
certainly spurious. Again, I suggest you build your system a different way
or find a better method of equilibration. It shouldn't be hard to keep
waters out if the system is built properly. If they then leak in over
(long) simulations, it might be relevant.

-Justin


On Thu, Jan 25, 2018 at 11:14 PM, Justin Lemkul  wrote:



On 1/25/18 12:17 PM, negar habibzadeh wrote:

How much time is needed to run ? i changed from 100 ps ( restrained

equilibration run ( nvt)) to 1 ns(1000ps) . but when i did npt (without
water and lipids restraints) again i saw water inside membrane.

I don't know. Such protocols are usually not necessary for a properly

prepared membrane. If you've got a huge amount of void space, I suggest
trying a different method to build the system, because perhaps the
starting
coordinates are simply poor.


-Justin


On Wed, Jan 24, 2018 at 10:51 PM, Justin Lemkul  wrote:


On 1/24/18 11:16 AM, negar habibzadeh wrote:

i did it  but when i removed the restraints from water to equilibrate


again
,(after new equilibration ) i saw some water molecules  inside the
membrane
again. what can i do ?

Let the restrained equilibration run longer. Make sure you're not


restraining the lipids in any way.

-Justin



On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul 
wrote:


On 1/24/18 5:02 AM, negar habibzadeh wrote:


hi . i am doing simulation of peptide in DOPC bilayer. i have
dopc.itp
,

dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,

peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701
   7.49241
-c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL
-nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit
0.1
(in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the
membrane.
how can i solve this problem ?

If there's lots of void space around the protein in the membrane,
then

you'll either need to prepare the system more carefully to prevent

such
voids, or do an equilibration with water molecules restrained in the
z-dimension only, to prevent them from diffusing into the membrane.
Then,
remove the restraints and equilibrate again.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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https://mai

Re: [gmx-users] gmx distance

[Justin Lemkul]

On 1/31/18 11:22 AM, rose rahmani wrote:

Hi,
This is md_pull.mdp

integrator   = md
dt   = 0.001
nsteps   = 400
nstxout  = 1000
nstvout  = 1000
nstfout  = 500
nstlog   = 500
nstenergy= 500
nstxtcout= 500
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = distance
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
---
pullx.xvg;

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.  4.287   1.76284
0.0500  4.287   1.75329
0.1000  4.287   1.74622
0.1500  4.287   1.73983
0.2000  4.287   1.73664
0.2500  4.287   1.7377
.
.

3999.7500   4.287   0.258632
3999.8000   4.287   0.258738
3999.8500   4.287   0.258955
3999.9000   4.287   0.260093
3999.9500   4.287   0.25843
4000.   4.287   0.258025
-
Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
whole
Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg

this is distwhole.xvg
0.0001.76307740.0185155   -0.0197599   -1.7628694
0.5001.7529889   -0.01330900.0135729   -1.7528858
1.0001.7453604   -0.03446920.0751038   -1.7434030
1.5001.7691813   -0.06215670.0087628   -1.7680674
.
.
3997.5001.61200060.9964043   -1.2400901   -0.2605782
3998.0001.61228910.9971979   -1.2404475   -0.2576084
3998.5001.61245740.9966092   -1.2406733   -0.2598433
3999.0001.61155650.9968075   -1.2396555   -0.2583475
3999.5001.61206160.9964568   -1.2404943   -0.2588253
4000.0001.61162940.9952377   -1.2410750   -0.2580390

as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
group (Protein and ZnS sheet) in last frame are too close to each other. so
why i see 1.611 in distwhole.xvg?

and could you please tell me what is the relevance of pullx.xvg to g_dist
output?as you see pullx.xvg ensure that distance between 2 group is
decreasing, so...?

is there anything i did not consider?


Your output is completely consistent. You're applying a biasing 
potential along the z-dimension only, so that's the only distance that 
mdrun cares about in establishing the reaction coordinate. The pullx.xvg 
file contains the COM coordinate of the "reference" group (group0) and 
in your case is just the z-coordinate, so that's the first data column. 
The second data column (dZ) is the displacement along the z-axis. Your 
COM distance results confirm this - your protein and ZnS are not exactly 
coincident; they have different x and y coordinates. But the z column in 
the distance output agrees with the pullx.xvg file (when considering the 
absolute value).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] MOVIE.pdb

[Justin Lemkul]

On 1/31/18 2:31 AM, Neha Gupta wrote:

Hi Justin,

I followed your protein-ligand complex tutorials to do the simulation.

I intend to run the simulation for 50 ns.

In the final md run section, can we modify the command like this

nstxout-compressed  = 50  ; write .xtc trajectory every 1000.0 ps


You have written the .xtc trajectory every 10 ps.

How would the above command change the o/p?


If you increase the number of steps between writing coordinates, you're 
saving fewer frames. With your setting, you're only saving every 1 ns, 
which is very infrequent. Make sure you save enough frames to see the 
behavior of interest and collect sufficient data.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] how to make index file for a complex which is composed of protein and a phosphotyrosine ligand

[Justin Lemkul]

On 1/31/18 6:38 AM, farial tavakoli wrote:

Dear gmx users
I need to calculate the energy binding of my complex, composed protein and a 
phosphotyrosine ligand, using g_mmpba, but when I wanna make an index file by 
this command:gmx make_ndx -f md_0_1.gro -o index.ndxand type :splitch 1 in 
order to separate the protein and phosphotyrosine ligand , face to this 
elements:
Group 0 ( System) has 67577 elements
Group 1 (    Protein) has  5290 elements
Group 2 (  Protein-H) has  2631 elements
Group 3 (    C-alpha) has   328 elements
Group 4 (   Backbone) has   984 elements
Group 5 (  MainChain) has  1310 elements
Group 6 (   MainChain+Cb) has  1619 elements
Group 7 (    MainChain+H) has  1624 elements
Group 8 (  SideChain) has  3666 elements
Group 9 (    SideChain-H) has  1321 elements
Group    10 (    Prot-Masses) has  5290 elements
Group    11 (    non-Protein) has 62287 elements
Group    12 (  Other) has    48 elements
Group    13 (    TP2) has    48 elements
Group    14 ( NA) has    11 elements
Group    15 (  Water) has 62228 elements
Group    16 (    SOL) has 62228 elements
Group    17 (  non-Water) has  5349 elements
Group    18 (    Ion) has    11 elements
Group    19 (    TP2) has    48 elements
Group    20 ( NA) has    11 elements
Group    21 ( Water_and_ions) has 62239 elements
Group    22 ( Protein_chain1) has  5204 elements
Group    23 ( Protein_chain2) has    86 elements

Group 23 is my ligand but without phosphotyrosine groups. Groups 13 & 19 are 
phosphotyrosine groups. I dont know how I can obtain my ligand with its 
ohosphotyrosine groups.is there anyone can help me?


Merge the two groups.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] gmx distance

[rose rahmani]

Hi,
This is md_pull.mdp

integrator   = md
dt   = 0.001
nsteps   = 400
nstxout  = 1000
nstvout  = 1000
nstfout  = 500
nstlog   = 500
nstenergy= 500
nstxtcout= 500
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = distance
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
---
pullx.xvg;

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.  4.287   1.76284
0.0500  4.287   1.75329
0.1000  4.287   1.74622
0.1500  4.287   1.73983
0.2000  4.287   1.73664
0.2500  4.287   1.7377
.
.

3999.7500   4.287   0.258632
3999.8000   4.287   0.258738
3999.8500   4.287   0.258955
3999.9000   4.287   0.260093
3999.9500   4.287   0.25843
4000.   4.287   0.258025
-
Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
whole
Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg

this is distwhole.xvg
   0.0001.76307740.0185155   -0.0197599   -1.7628694
   0.5001.7529889   -0.01330900.0135729   -1.7528858
   1.0001.7453604   -0.03446920.0751038   -1.7434030
   1.5001.7691813   -0.06215670.0087628   -1.7680674
.
.
3997.5001.61200060.9964043   -1.2400901   -0.2605782
3998.0001.61228910.9971979   -1.2404475   -0.2576084
3998.5001.61245740.9966092   -1.2406733   -0.2598433
3999.0001.61155650.9968075   -1.2396555   -0.2583475
3999.5001.61206160.9964568   -1.2404943   -0.2588253
4000.0001.61162940.9952377   -1.2410750   -0.2580390

as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
group (Protein and ZnS sheet) in last frame are too close to each other. so
why i see 1.611 in distwhole.xvg?

and could you please tell me what is the relevance of pullx.xvg to g_dist
output?as you see pullx.xvg ensure that distance between 2 group is
decreasing, so...?

is there anything i did not consider?

Thank you so much
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Re: [gmx-users] Grompp warning about topology constrains

[Ahmed Mashaly]

Thanks Justin Kind Regards,Ahmed Mashaly



  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Tuesday, January 30, 2018 6:00 PM
 Subject: Re: [gmx-users] Grompp warning about topology constrains
   


On 1/30/18 5:46 AM, Ahmed Mashaly wrote:
>
> Thanks Justin ... The topology seems fine to me
>
> The inputs are in this link incase of the text is messed again
> https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR
>
>
>
> title = NVT
> define = -DPOSRES ;
>
> ; Run parameters
> integrator = md
> dt = 0.002
> nsteps = 25
>
> ; Output control
> nstlog = 500
> nstxout = 500
> nstvout = 500
> nstfout = 500
> nstcalcenergy = 10
> nstenergy = 500
>
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 2
> lincs_order = 4
> shake-tol        = 1e-05
>
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid
> nstlist = 10
> rlist = 1.0
> rvdw = 1.0
> vdwtype = Cut-off
> rcoulomb = 1.0
>
> ; Electrostatics
> coulombtype = pme
> pme_order = 4
> fourierspacing = 0.16
>
> ; Temperature coupling
> tcoupl = V-rescale
> tc_grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
>
> ; Pressure coupling
> pcoupl = no
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Dispersion correction
> DispCorr = EnerPres
>
> ;
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
>
>
>
>
>
> The last lines of toplogy:

As I said before, the line numbers here and their contents are irrelevant.

The error message and its solution are quite clear. You have at least 
one angle between some atoms i-j-k, in which the masses of atoms i and k 
differ by at least a factor of 13. In this instance, you shouldn't be 
constraining all bonds. Set constraints = h-bonds and move ahead. The 
only force field that I know of that requires all bonds to be 
constrained is GROMOS, all others normally only constrain bonds to H.

-Justin

> 79101 [ moleculetype ]
> 79102 ; Name nrexcl
> 79103 SOL 3
> 79104
> 79105 [ atoms ]
> 79106 ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 79107 ; residue 1 WAT rtp WAT q 0.0
> 79108 1 OW 1 SOL OW 1 -0.834000 16. ; qtot -0.8340
> 79109 2 HW 1 SOL HW1 2 0.417000 1.0080 ; qtot -0.4170
> 79110 3 HW 1 SOL HW2 3 0.417000 1.0080 ; qtot 0.
> 79111
> 79112 #ifdef FLEXIBLE
> 79113
> 79114 [ bonds ]
> 79115 ; ai aj funct c0 c1 c2 c3
> 79116 2 3 1 0.15136 462750.40
> 79117 1 2 1 0.09572 462750.40
> 79118 1 3 1 0.09572 462750.40
> 79119
> 79120
> 79121 #else
> 79122
> 79123 [ settles ]
> 79124 ; i funct doh dhh
> 79125 1 1 0.09572 0.15136
> 79126
> 79127 #endif
> 79128
> 79129 [ exclusions ]
> 79130 1 2 3
> 79131 2 1 3
> 79132 3 1 2
> 79133
> 79134 [ system ]
> 79135 ; Name
> 79136 Generic title
> 79137
> 79138 [ molecules ]
> 79139 ; Compound #mols
> 79140 system1 1
> 79141 system2 1
> 79142 system1 1
> 79143 system2 1
> 79144 system1 1
> 79145 system2 1
> 79146 NA 3
> 79147 SOL 49664
>
>
>
>
>  
> Kind Regards,
> Ahmed
>
>
>
>
>
> 
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Sent: Tuesday, January 30, 2018 2:14 AM
> Subject: Re: [gmx-users] Grompp warning about topology constrains
>
>
>
>
>
> On 1/29/18 11:03 AM, Ahmed Mashaly wrote:
>> Hi,
>> I have set up my parameters with tleap, converted to gromacs with Acpype, 
>> did the minimization.
>>
>>
>> For NVT, when I use grompp, this warning appears:
>> WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of 
>> an angle, connected by constraints and  with masses that differ by more than 
>> a factor of 13. This means that  there are likely dynamic modes that are 
>> only very weakly coupled. To  ensure good equipartitioning, you need to 
>> either not use constraints on  all bonds (but, if possible, only on bonds 
>> involving hydrogens) or use  integrator = sd or decrease one or more 
>> tolerances:  verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS 
>> order >=  4 or SHAKE tolerance <= 1e-05
>>
>> But in .top file there in this line (the last one) there is no such a thing.
> The error appears at the end of topology parsing, so it reports the last
> line as being the source, but that's not correct. It's just a reflection
> of the fact that you're doing something unstable somewhere in the topology.
>
>> It worked when I changed the integrator to sd or when I changed the 
>> constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order 
>> >= 4 or SHAKE tolerance <= 1e-05
>>
>>
>> I even deleteddefine                  = -DPOSRES
>> from the .mdp file and got the same warning
> Position restraints have nothing to do with bond constraints.
>
> The text below is basically unintelligible. Please use proper line
> wrapping in your email client.
>
> -Justin
>
>
>> this is my input file:itle                  = NVT define                  = 
>> -DPOSRES ; Run parametersintegrator              = md      dt                
>>       = 0.002    nsteps                  = 

[gmx-users] Help in stretching membrane

[Rajeswari A.]

Dear gromacs users,

I am totally new to membrane simulation.

I wish to simulate a membrane-protein system with applied pressure (say
-100 bar). I have read from the user forums and gromacs manual that I can
achieve this either by semiisotropic coupling where I can explicitly give
the pressure on xy plane as -100. or by using surface tension coupling.

I am interested to go with the surface tension coupling. But I am not sure
how should I set the mdp parameters for achieving the required pressure.
Moreover, what parameters do I need to validate post simulation?

Can Somebody please guide me in these regards?

Thanks a lot!


Rajeswari A,
SERB National Postdoctoral Fellow
Molecular Biophysics,
Indian Institute of Science,
Bangalore, India - 560 012
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[gmx-users] how to make index file for a complex which is composed of protein and a phosphotyrosine ligand

[farial tavakoli]

Dear gmx users
I need to calculate the energy binding of my complex, composed protein and a 
phosphotyrosine ligand, using g_mmpba, but when I wanna make an index file by 
this command:gmx make_ndx -f md_0_1.gro -o index.ndxand type :splitch 1 in 
order to separate the protein and phosphotyrosine ligand , face to this 
elements:
Group 0 ( System) has 67577 elements
Group 1 (    Protein) has  5290 elements
Group 2 (  Protein-H) has  2631 elements
Group 3 (    C-alpha) has   328 elements
Group 4 (   Backbone) has   984 elements
Group 5 (  MainChain) has  1310 elements
Group 6 (   MainChain+Cb) has  1619 elements
Group 7 (    MainChain+H) has  1624 elements
Group 8 (  SideChain) has  3666 elements
Group 9 (    SideChain-H) has  1321 elements
Group    10 (    Prot-Masses) has  5290 elements
Group    11 (    non-Protein) has 62287 elements
Group    12 (  Other) has    48 elements
Group    13 (    TP2) has    48 elements
Group    14 ( NA) has    11 elements
Group    15 (  Water) has 62228 elements
Group    16 (    SOL) has 62228 elements
Group    17 (  non-Water) has  5349 elements
Group    18 (    Ion) has    11 elements
Group    19 (    TP2) has    48 elements
Group    20 ( NA) has    11 elements
Group    21 ( Water_and_ions) has 62239 elements
Group    22 ( Protein_chain1) has  5204 elements
Group    23 ( Protein_chain2) has    86 elements

Group 23 is my ligand but without phosphotyrosine groups. Groups 13 & 19 are 
phosphotyrosine groups. I dont know how I can obtain my ligand with its 
ohosphotyrosine groups.is there anyone can help me?
best Farial
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Re: [gmx-users] How to modify Lorentz−Berthelot combining rules?

[David van der Spoel]

Den 2018-01-31 kl. 00:12, skrev Fariba Asadi:

Hi,



I am using GROMACS to simulate water/methane system. I used
Lorentz−Berthelot combining rules:

σMO = (σM + σO)/2

εMO = χ (εMεO)^0.5

where σ and ε are parameters in the Lennard-Jones potential function, and χ
is a factor used to adjust the strength of cross interaction between
methane and water.



Does anyone know how to change χ to 1.07?



Easiest is to just add a section
[ nonbond_params ]
where you specify all the parameters yourself in a pairwise fashion.




I will be grateful for any suggestions.

Fariba




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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