[gmx-users] The PMF curve is asymmetric (However many results of membrane penetration are symmetric)

[ygdcn]

Hi all: 
 
I tried to use MD simulation to pull a drug across the POPC membrane and to 
calculate PMF. I obtained the PMF curve following the guide 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/)
 
I found the PMF curve increases as the penetration process proceeds. The PMF 
curve is asymmetric, it increases in the whole time. However many results of 
membrane penetration are symmetric, e.g. increase earlier and decrease lately 
(X=0 in the central) . How can I get the similar result? There are examples of 
this in the GROMACS manual (see, e.g. the diagram for the cylinder geometry in 
the case of layered systems), but it is too difficult for me to understand it. 
I also read the answer 
(https://www.researchgate.net/post/How_to_pull_a_solute_across_liquid-liquid_interface).
  I am sure that a drug and a membrane will come closer when I used the 
negative pull rate. But I have some doubts whether the drug can continue to 
move ahead and leave the membrane after it arrive at the central of membrane.

Best regards, 



Best regards, 
祝  安好
--
Guodong YE 
Ph.D,  Professor
Department of Pharmaceutical Chemistry
School of Pharmaceutical Sciences
Guangzhou Medical University
Address: Guangzhou Medical University (Panyu Campus) 
Xinzao Town, Panyu District, Guangzhou, China, 511436
--
叶国东，博士，教授
广州医科大学 药学院 化学教研室
广州市番禺区新造镇


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Re: [gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

thanks. problem resolved.

On 21 Feb 2018 08:13, "Justin Lemkul"  wrote:

>
>
> On 2/20/18 9:50 PM, neelam wafa wrote:
>
>> Dear gmx users
>>
>> I am still stuck at this point.
>> error obtained is this
>> Fatal error:
>> number of coordinates in coordinate file (solv.gro, 32803)
>>   does not match topology (topol.top, 32818)
>> There is a difference of 15. I think its not considering the ligand as 15
>> is i think for ligand. the ligand. the entries of ligand in gro file are
>> these.
>> 15
>>  1JZ4  C4   1   2.946  -2.601   0.141
>>  1JZ4  C14  2   3.009  -2.568   0.005
>>  1JZ4  C13  3   2.965  -2.664  -0.107
>>  1JZ4  C12  4   2.834  -2.642  -0.154
>>  1JZ4  C11  5   2.734  -2.734  -0.116
>>  1JZ4  H11  6   2.753  -2.810  -0.040
>>  1JZ4  C7   7   2.606  -2.727  -0.176
>>  1JZ4  H7   8   2.529  -2.798  -0.147
>>  1JZ4  C8   9   2.578  -2.628  -0.273
>>  1JZ4  H8  10   2.479  -2.624  -0.319
>>  1JZ4  C9  11   2.677  -2.536  -0.311
>>  1JZ4  H9  12   2.655  -2.460  -0.387
>>  1JZ4  C10 13   2.804  -2.543  -0.251
>>  1JZ4  OAB 14   2.900  -2.451  -0.285
>>  1JZ4  HAB 15   2.863  -2.389  -0.354
>> 0.68000   0.68000   0.68000
>>
>> Help me out please.
>>
>
> Looks like you probably didn't copy the ligand coordinates into the
> topology. The topology thinks it's there and the coordinates say it's not.
> The solution to this error is always the same: proper bookkeeping.
>
> -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] selection of the type of box in molecular dynamics in GROMACS

[Vikram Dalal]

Hi everyone,




I want to know that on what basis we have to select the specific type of a box 
for a particular protein during molecular dynamics in GROMACS ?




Thank you in advance. 


--
Thanks & Regards,
VIKRAM DALAL
Research Scholar
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Re: [gmx-users] query about coul-SR

[Saumyak Mukherjee]

Thanks for your reply Alex.



‌

On 23 February 2018 at 02:01, Alex  wrote:

> No, this is the particle-particle cutoff portion in the particle-particle
> + particle-mesh scheme. Unless the size of your entire protein is smaller
> than rcoulomb.
>
> Alex
>
>
> On 2/22/2018 1:07 PM, Saumyak Mukherjee wrote:
>
>> Dear Users,
>>
>> In the output of gmx energy, coul-SR means short range Coulomb
>> interactions. So if I have coul-SR for a protein, does it give the total
>> self-interaction energy (Coulomb) of the protein?
>>
>> Any help is much appreciated.
>>
>> Thanks & regards,
>>
>> *Saumyak Mukherjee*
>>
>> Senior Research Fellow,
>> Prof. Biman Bagchi's Lab,
>> Solid State and Structural Chemistry Unit,
>> Indian Institute of Science,
>> Bangalore - 560012,
>> Karnataka, India.
>>
>>
>>
>>
>>
>> ‌
>>
>
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-- 
Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.
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Re: [gmx-users] query about coul-SR

[Alex]

No, this is the particle-particle cutoff portion in the 
particle-particle + particle-mesh scheme. Unless the size of your entire 
protein is smaller than rcoulomb.


Alex


On 2/22/2018 1:07 PM, Saumyak Mukherjee wrote:

Dear Users,

In the output of gmx energy, coul-SR means short range Coulomb
interactions. So if I have coul-SR for a protein, does it give the total
self-interaction energy (Coulomb) of the protein?

Any help is much appreciated.

Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.





‌


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[gmx-users] query about coul-SR

[Saumyak Mukherjee]

Dear Users,

In the output of gmx energy, coul-SR means short range Coulomb
interactions. So if I have coul-SR for a protein, does it give the total
self-interaction energy (Coulomb) of the protein?

Any help is much appreciated.

Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.





‌
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[gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

[ZHANG Cheng]

Dear Gromacs,
The scount.xvg file was obtained after running


echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map 
ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg 
-tu ns


The secondary structures listed are:
'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix'


I ran the command for different proteins. It surprised me that the last 
'5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not 
have the '5-Helix', but why not just show them as 0? Can this be improved?


Because I am using a script to read the scount.xvg files, so I want all the 
files have the same format.


Thank you.


Yours sincerely
Cheng
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[gmx-users] Example of arithmetic expression in gmx select?

[Viveca Lindahl]

Hi all,

I'm trying to do selections that require addition, which is supposed to be
supported according to 'gmx help selections'. I get syntax error however
when doing from within 'gmx select':

a=1+1
resid a

What is the right syntax for achieving a=2...?

Thanks,
Viveca
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[gmx-users] calculating force for a restrained structure

[Ali Shomali]

 Dear Justin and all GROMACS users,

I'm simulating a nano tube which is placed in a lipid system. the nano tube
is completely restrained to halt rotation or COM movement. Now, I intend to
calculate the force applied from lipid layer to nanotube. the question is
how can i eliminate the effect of spring force from restraining option? can
i extract the force of a specific group from the net force applied to
nanotube?


Thank you for any help,

Ali
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[gmx-users] problems with the output of pullx

[Alfredo E. Cardenas]

Hi,
I am using gromacs to get the PMF of a peptide of  about 20 amino acids, moving 
inside of a bilayer membrane. After pulling the peptide inside the membrane now 
I am using  pull-coord1-type = umbrella
and pull-coord1-geometry  = distance to sample configurations in each window 
for the umbrella simulations along the z axis (axis perpendicular to the 
membrane surface). Runs finish ok, no error messages. The problem is that when 
I looked at the contents of the pullx file I observed spikes (up to 5 or more 
Angstroms) in the z coordinate separating the center of mass of the peptide 
from the membrane center. But when I extract the z coordinates of the center of 
mass of the two groups and compute the difference the values look reasonable 
with no spikes.

Here an example (it starts good):
time (ps)   from pullx  from traj analysis

   20.000  0.475923002  0.475919992
   200010.000  0.498394012  0.498389989
   200020.000  0.527589977  0.527589977
   200030.000  0.491834015  0.493739992
   200040.000  0.485377997  0.485379994
   200050.000  0.488474995  0.488469988
   200060.000  0.507991016  0.507990003
   200070.000  0.475095987  0.475100011
   200080.000  0.465889990  0.465889990
   200090.000  0.515878975  0.515879989
   200100.000  0.501435995  0.501429975
   200110.000  0.505191982  0.505190015

Here a bad section:

   214000.000  0.427343011  0.601450026
   214010.000  0.484564990  0.545799971
   214020.000  0.530139029  0.603110015
   214030.000  0.176231995  0.650319993
   214040.000  0.342045009  0.637109995
   214050.000  0.181202993  0.636659980
   214060.000  0.338808000  0.595300019
   214070.000  0.442301005  0.547529995
   214080.000  0.396046013  0.565050006
   214090.000  0.431407988  0.538460016
   214100.000  0.402586013  0.56825
   214110.000  0.438223004  0.575810015

Then good again:

   23.000  0.477869004  0.477869987
   230010.000  0.511840999  0.511839986
   230020.000  0.469146013  0.469150007
   230030.000  0.480194002  0.480190009
   230040.000  0.525618017  0.525619984
   230050.000  0.498955995  0.498950005
   230060.000  0.489230990  0.489230007
   230070.000  0.531931996  0.531930029
   230080.000  0.535376012  0.535380006
   230090.000  0.488822013  0.48883
   230100.000  0.510704994  0.510699987
   230110.000  0.524537981  0.524540007
   230120.000  0.513199985  0.513189971

This problem happens in most umbrella windows that I have examined, sometimes 
several times during the long trajectories I am running. The pullf output also 
have those spikes.

Here is the mdp file I am using:

integrator  = md
dt  = 0.002
nsteps  = 5000
nstlog  = 1
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy   = 500
nstenergy   = 500
;
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 = PROT   MEMB   SOL_ION
tau_t   = 1.01.01.0
ref_t   = 303.15 303.15 303.15
;
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
continuation= yes
;
nstcomm = 500
comm_mode   = linear
comm_grps   = PROT_MEMB   SOL_ION
;
refcoord_scaling= com
;
pull= yes
pull-coord1-type= umbrella
pull-coord1-geometry= distance
pull-coord1-dim = N N Y
pull-ngroups= 2
pull-ncoords= 1
pull-coord1-groups  = 1 2
pull-group1-name= MEMB
pull-group2-name= PROT
pull-coord1-init= 0.400
pull-coord1-k   = 1000; kJ mol^-1 nm^-2
pull-nstxout= 500; every 1 ps
pull-nstfout= 500; every 1 ps


I am not sure what is wrong here. It seems a bug to me.


Here is the header of the log file:

Log file opened on Thu Feb 15 11:09:05 2018
Host: sb202  pid: 254782  rank ID: 0  number of ranks:  112
  :-) GROMACS - mdrun_mpi, 2016.4 (-:



GROMACS:  mdrun_mpi, version 

Re: [gmx-users] New in the mailing list

[Mark Abraham]

Hi,

Use the same version of GROMACS for converting the tpr as you used for
running the simulation. Old code can't know about new modules, etc.

Mark

On Thu, Feb 22, 2018, 14:37 Giordano Perini 
wrote:

> Hello everyone,
> I've just joined this mailing list in order to understand how to solve a
> problem while extending a simulation. I am trying to generate a new tpr
> file via command line:
>
> gmx convert-tpr  -s [old].tpr -extend [timeneeded] -o new.tpr
>
> BUT, when compiling, it tells me:
>
> reading tpx file (md_0_1.tpr) version 110 with version 103 program
>
> What can I do to solve that "fatal error"?
>
> Thank you for your kindness,
> Giordano Perini, PhD student, Institute of Physics, Catholic University of
> Sacred Heart, Rome.
> --
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[gmx-users] New in the mailing list

[Giordano Perini]

Hello everyone,
I've just joined this mailing list in order to understand how to solve a
problem while extending a simulation. I am trying to generate a new tpr
file via command line:

gmx convert-tpr  -s [old].tpr -extend [timeneeded] -o new.tpr

BUT, when compiling, it tells me:

reading tpx file (md_0_1.tpr) version 110 with version 103 program

What can I do to solve that "fatal error"?

Thank you for your kindness,
Giordano Perini, PhD student, Institute of Physics, Catholic University of
Sacred Heart, Rome.
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