date:20170607

Finally I managed to find the exact syntax for the rdf calculation by
adding " -ref 'com of group g1'  " at the end of the command-line:
gmx rdf -f cgs.gro   -s cgs.tpr   -o rdf.xvg  -xy  -ref 'com of group g1'

On Thu, Jun 8, 2017 at 12:56 AM, Sajjad Kavyani 
wrote:

> Dear experts,
> Recently I ask a question entitled "RDF of a group around CNT axis" in
> the mailing list in order to find proper command-line for it it turns out
> that the "-xy" option can help
> But I encounter an unusual problem therefore I decided to ask another
> question
>
> It turns out that the gmx rdf cannot find the com coordinate of the CNT
> (as reference) because as I choose different command-lines with various
> "-selrpos" arguments, all of the results gave me EXACTLY the SAME result
> which all of them are wrong! Commands like:
> gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg
> gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos res_com
> gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos res_cog
> gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos mol_com
> gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos mol_cog
> (CNT group has been chosen for both groups is gmx rdf)
>
> But when I manually placed a single particle in the COM of the cnt (in the
> cgs.gro) and then select this single particle as reference group, the gmx
> rdf resulted the desired value!
>
>
> Could you please help me to manage the problem?
> How to tell the gmx rdf in order to find com of cnt without manually
> placing a single particle in the input file?
>
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[gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group

Dear experts,
Recently I ask a question entitled "RDF of a group around CNT axis" in the
mailing list in order to find proper command-line for it it turns out that
the "-xy" option can help
But I encounter an unusual problem therefore I decided to ask another
question

It turns out that the gmx rdf cannot find the com coordinate of the CNT (as
reference) because as I choose different command-lines with various
"-selrpos" arguments, all of the results gave me EXACTLY the SAME result
which all of them are wrong! Commands like:
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos res_com
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos res_cog
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos mol_com
gmx rdf -f cgs.gro  -s md.tpr -xy  -o rdf.xvg -selrpos mol_cog
(CNT group has been chosen for both groups is gmx rdf)

But when I manually placed a single particle in the COM of the cnt (in the
cgs.gro) and then select this single particle as reference group, the gmx
rdf resulted the desired value!


Could you please help me to manage the problem?
How to tell the gmx rdf in order to find com of cnt without manually
placing a single particle in the input file?
-- 
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Re: [gmx-users] deltaG shifts in g_wham




On 6/7/17 4:18 PM, Alex wrote:

Hi all,

I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
with a narrow pore and an ion. The configurations correspond to various
heights "above" the membrane (0 to 1.5 nm).

In one case, the ion is K+, in another Na+. In both cases the results are
fairly reasonable, but there is a bit of a numerical caveat.

For sodium, the free energy away from the pore is close to zero and
considerably negative inside the pore, as one might expect. For potassium
(the input files are nearly identical), the free energy far away from the
pore is a considerable _positive_ value and zero inside the pore. I do
realize that absolute values are meaningless and I can always "shift" the
results to correspond to near-zero far away from the reactive site (and
when I do, I even have reasonable agreement with experiment). However, I
want to understand what is happening with the utility. My simulation times
are quite moderate (1 ns for each config).

Can someone help?



WHAM sets the "left-most" window (i.e. smallest value of zeta) to zero and 
calculates all free energy values relative to that.  This is why you can offset 
at any given point.


-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] deltaG shifts in g_wham

2017-06-07 Thread Alex

Hi all,

I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
with a narrow pore and an ion. The configurations correspond to various
heights "above" the membrane (0 to 1.5 nm).

In one case, the ion is K+, in another Na+. In both cases the results are
fairly reasonable, but there is a bit of a numerical caveat.

For sodium, the free energy away from the pore is close to zero and
considerably negative inside the pore, as one might expect. For potassium
(the input files are nearly identical), the free energy far away from the
pore is a considerable _positive_ value and zero inside the pore. I do
realize that absolute values are meaningless and I can always "shift" the
results to correspond to near-zero far away from the reactive site (and
when I do, I even have reasonable agreement with experiment). However, I
want to understand what is happening with the utility. My simulation times
are quite moderate (1 ns for each config).

Can someone help?

Thanks,

Alex
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Re: [gmx-users] gmx insert-molecules



Please do not reply to the whole digest.

On 6/7/17 2:46 PM, Shi Li wrote:


On 6/7/17 1:20 PM, Li, Shi wrote:

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?



Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated
box of molecule A.  Works every time.

-Justin


Thank you Justin,

In this case, I will need to apply a full equilibrium process (em, nvt, npt) to 
the new system, is that right?

I am trying to avoid the long step of equilibrium as I have many systems 
corresponding to different concentrations. I was thinking if I replace a small 
number of molecule A with molecule B (the system A is very large and 
pre-equilibriumed) then I only need to apply a short time-step of NPT in order 
to let the system expand or shrink. Then I can use the new system to continue 
replacing A with B to generate a new concentration. Is this practical?

The problem is when B is slightly larger than A, I can’t insert the same number 
of B into the system. Is there way to avoid the overlapping or force the 
molecule in?
You can reduce the vdW radius of atoms to *try* to force the molecules to fit, 
but then all you've done is introduce bad clashes that have to be subjected to 
minimization and re-equilibration.  So at that point, all you've done is build 
your system in the most inefficient way possible.  By trying to avoid 
equilibration, you've necessitated it :)


Build the system the robust way - solute first, then solvent.  It's ultimately 
less work and less prone to failure.


-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] Cylinder pulling through bilayer

2017-06-07 Thread Gmx QA

Dear list

I am attempting to pull a small molecule though a bilayer using the pull
geometry cylinder with gromacs v 2016.

This is the relevant portion of my mdp-file:

pull  = yes
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups   = 1 2
pull-group1-name = LIG
pull-group2-name = MEM
pull-coord1-type = umbrella
pull-coord1-geometry = cylinder
pull-coord1-rate = 0.1
pull-coord1-vec  = 0 0 1
pull-coord1-k= 1000
pull-coord1-start= yes
pull-coord1-init = 0
pull-cylinder-r  = 1.5

The pull-rate is very fast because I'm only doing preliminary test. At the
start, the drug molecule is in -z position compared to the membrane.

When doing grompp:

$ gmx grompp -f umbrella_md_test.mdp -c npt.gro -p topol.top -o
pull_test.tpr

The output makes no sense:
Using a fourier grid of 72x72x192, spacing 0.113 0.113 0.111
Pull group  natoms  pbc atom  distance at start  reference at t=0
   13618
   2 32500 64286-nan nm   -nan nm
Estimate for the relative computational load of the PME mesh part: 0.44
This run will generate roughly 14 Mb of data


I.e. nan's for distance. If I however switch in the mdp file so that
pull-group1-name = MEM and pull-group2-name = LIG, the distance gets
correctly calculated. But this does not seem to be what is prescribed in
the manual for cylinder pulling, where is says that the cylinder is formed
from the first group (should be the drug molecule) and through the com of
the reference group (the membrane in my case),

I think there is something I am missing?

Thanks!
/PK
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Re: [gmx-users] gmx insert-molecules

2017-06-07 Thread Shi Li


> 在 2017年6月7日，13:31，gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道：
> 
> Send gromacs.org_gmx-users mailing list submissions to
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> 
> 
> Today's Topics:
> 
>   1. Re: Simulate protein at subzero condition in aqueous buffer
>  (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
>   2. Re: Simulate protein at subzero condition in aqueous buffer
>  (Jo?o Henriques)
>   3. gmx insert-molecules (Li, Shi)
>   4. Re: gmx insert-molecules (Justin Lemkul)
>   5. Re: Simulate protein at subzero condition in aqueous buffer
>  (Jo?o Henriques)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 8 Jun 2017 01:07:40 +0800
> From: "=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=" <272699...@qq.com>
> To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="
>   
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
>   aqueous buffer
> Message-ID: 
> Content-Type: text/plain; charset="ISO-8859-1"
> 
> Dear Justin,
> Thank you very much. I will try the possible water models.
> 
> 
> Do you know if there are water models to resemble frozen state?
> 
> 
> Yours sincerely
> Cheng
> 
> 
> 
> 
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Thu, Jun 8, 2017 00:50 AM
> To:  "ZHANG Cheng"<272699...@qq.com>; 
> "gromacs.org_gmx-users"; 
> 
> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
> 
> 
> 
> Dear Joao,
> Thank you for your help and the paper link.
> 
> 
> I was following Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
> On that page, it says "spc216.gro as the solvent configuration for SPC, 
> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) 
> after the solvation step. So I assume "spc216.gro" refer to all the 
> three-point water models?
> 
> 
> I am trying to see if my protein will be denatured in cold condition. 
> 
> 
> Yours sincerely
> Cheng
> 
> 
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Wed, Jun 7, 2017 10:01 PM
> To:  "gromacs.org_gmx-users"; 
> Cc:  "ZHANG Cheng"<272699...@qq.com>; 
> Subject:  Simulate protein at subzero condition in aqueous buffer
> 
> 
> 
> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous buffer, 
> to see if it becomes more stable than the elevated temperature (e.g. 65 C). 
> Can I ask what is the valid temperature range for water "spc216.gro" ? If I 
> run the simulation at -40 C, does it still assume the system as liquid state 
> instead of frozen state? Thank you.
> 
> 
> Yours sincerely
> Cheng
> 
> --
> 
> Message: 2
> Date: Wed, 7 Jun 2017 19:15:58 +0200
> From: Jo?o Henriques 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
>   aqueous buffer
> Message-ID:
>

Re: [gmx-users] RDF of a group around CNT axis

I noticed that the gmx rdf some how cannot find the center of mass (COM)
for the CNT because after that I manually put a single particle in the COM
of the CNT and calculated the rdf around it (with -xy option), the gmx rdf
resulted the expected value which is a sharp peak at the radius of the cnt.
I tested all the -selrpos arguments but none of them could find the COM of
the CNT
Could you please help me to manage the problem ?

Regards
Sajjad

On Wed, Jun 7, 2017 at 7:19 PM, Sajjad Kavyani 
wrote:

> Dear Srinivas,
> That's absolutely right, I want to calculate the RDF of a certain
> group around the central axis of a nanotube.
> And as I know that the RDF of the CNT around its axis is just a sharp peak
> at the radius, I just tested the command-line parameters for this case, to
> specify that which command-line should be used.
>
> And honestly I do not understand the last sentence of your reply, could
> you please specify that after isolating the desired group, what
> command-line I should use?
>
> Sincerely,
> Sajjad
>
>
>
> On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI <
> scm...@scarletmail.rutgers.edu> wrote:
>
>> If I understand you correctly: you want to calculate the RDF of a certain
>> group (NOT part of the nanotube) around the central axis of a nanotube?
>>
>> The way I do these calculations is to use the gmx trjconv tool to isolate
>> a
>> trajectory file of ONLY the gropus I am interested in and run my
>> calculations on that.
>> If you expect to see one peak but see many that might mean that the RDF is
>> picking up groups that you don't want it to.
>>
>> Hope that helps,
>> Srinivas
>>
>> On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
>> wrote:
>>
>> > Dear experts,
>> > I want to calculate rdf of a certain group around the axis of a cnt,
>> but I
>> > do not know what are the proper parameters to choose in the
>> command-line.
>> > To test the parameters, I calculated the rdf of cnt itself around its
>> axis
>> > which must be a sharp peak at the cnt radius.
>> > I tested the following: (both selection groups of reference and rdf are
>> > CNT)
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
>> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
>> >
>> > BUT all the results are the same!!! and surprisingly they have multiple
>> > sharp peaks at different ranges, which I expected just one peak at the
>> > radius of the CNT 
>> > It is notable that the CNT is aligned to z axis.
>> > (the first two peaks are listed below):
>> >
>> >   0.000 211939.438
>> >   0.002 53771.996
>> >   0.004 11278.401
>> >   0.006 3935.633
>> >   0.008 1782.280
>> >   0.010  809.616
>> >   0.012  584.723
>> >   0.014  536.531
>> >   0.016  292.361
>> >   0.018  149.929
>> >   0.020   94.455
>> >   0.022   00.000
>> >   ...
>> >   ...
>> >   ...
>> >   0.11800.000
>> >   0.1200.375
>> >   0.1222.212
>> >   0.1240.725
>> >   0.1266.069
>> >   0.128   36.545
>> >   0.130  114.868
>> >   0.132  278.390
>> >   0.134 1669.916
>> >   0.136 2360.069
>> >   0.138  346.139
>> >   0.140  183.770
>> >   0.142   39.277
>> >
>> > Could you please explain to me that what should I do?
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
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>> >
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>
>
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Joao,
Thank you very much for your support. I am following Justin's tutorial but 
simulating a fragment of antibody (Fab).


I will try the different water models.


Yours sincerely
Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Thu, Jun 8, 2017 01:07 AM
To:  "gromacs.org_gmx-users"; 

Subject:  Re: Re:  Simulate protein at subzero condition in aqueous buffer



Dear Justin,
Thank you very much. I will try the possible water models.


Do you know if there are water models to resemble frozen state?


Yours sincerely
Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Thu, Jun 8, 2017 00:50 AM
To:  "ZHANG Cheng"<272699...@qq.com>; 
"gromacs.org_gmx-users"; 

Subject:  Re: Simulate protein at subzero condition in aqueous buffer



Dear Joao,
Thank you for your help and the paper link.


I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, 
or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the 
solvation step. So I assume "spc216.gro" refer to all the three-point water 
models?


I am trying to see if my protein will be denatured in cold condition. 


Yours sincerely
Cheng


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Wed, Jun 7, 2017 10:01 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  Simulate protein at subzero condition in aqueous buffer



Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to 
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I 
ask what is the valid temperature range for water "spc216.gro" ? If I run the 
simulation at -40 C, does it still assume the system as liquid state instead of 
frozen state? Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

2017-06-07 Thread João Henriques

Just one more thing. If you're following Justin's tutorial, I guess you're
using lysozyme. This protein will not deviate very much from it's crystal
structure at 27ºC, let alone at -40ºC (*in the context of a molecular
dynamics simulation**). I understand that it may be possible to
experimentally unfold this protein reversibly using low temperature and
high pressure, but this may be unfeasible to perform using a regular
protein force field and water model. It will not behave as you expect.

* I should add that this is a very stable protein and the disulfide bonds
(which cannot be broken during the simulation) make it almost impossible to
unfold it completely at any temperature using molecular dynamics.

/J



On Wed, Jun 7, 2017 at 7:15 PM, João Henriques  wrote:

> Higher complexity water models such as TIP5P and so on are able to better
> reproduce bulk water properties (please check the paper I linked in my
> earlier email). However, these models require more computational effort
> (due to the increased number of interactions) and may not work well in
> conjunction with a protein (many protein force fields were developed to be
> used with specific water models). As Justin said, none of them gets
> everything right.
>
> /J
>
> On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote:
>
>> Dear Justin,
>> Thank you very much. I will try the possible water models.
>>
>>
>> Do you know if there are water models to resemble frozen state?
>>
>>
>> Yours sincerely
>> Cheng
>>
>>
>>
>>
>> -- Original --
>> From:  "ZHANG Cheng";<272699...@qq.com>;
>> Date:  Thu, Jun 8, 2017 00:50 AM
>> To:  "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"> s.org_gmx-us...@maillist.sys.kth.se>;
>>
>> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
>>
>>
>>
>> Dear Joao,
>> Thank you for your help and the paper link.
>>
>>
>> I was following Justin's tutorial
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/lysozyme/03_solvate.html
>> On that page, it says "spc216.gro as the solvent configuration for SPC,
>> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
>> after the solvation step. So I assume "spc216.gro" refer to all the
>> three-point water models?
>>
>>
>> I am trying to see if my protein will be denatured in cold condition.
>>
>>
>> Yours sincerely
>> Cheng
>>
>>
>> -- Original --
>> From:  "ZHANG Cheng";<272699...@qq.com>;
>> Date:  Wed, Jun 7, 2017 10:01 PM
>> To:  "gromacs.org_gmx-users";
>> Cc:  "ZHANG Cheng"<272699...@qq.com>;
>> Subject:  Simulate protein at subzero condition in aqueous buffer
>>
>>
>>
>> Dear Gromacs,
>> I would like to simulate the protein at subzero condition in aqueous
>> buffer, to see if it becomes more stable than the elevated temperature
>> (e.g. 65 C). Can I ask what is the valid temperature range for water
>> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
>> system as liquid state instead of frozen state? Thank you.
>>
>>
>> Yours sincerely
>> Cheng
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] gmx insert-molecules




On 6/7/17 1:20 PM, Li, Shi wrote:

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?



Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated 
box of molecule A.  Works every time.


-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] gmx insert-molecules

2017-06-07 Thread Li, Shi

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?

Or, is there a way to ignore the overlapping of molecules? In that case,
even the inserted molecule is overlapping with surrounding molecules, it
can still be inserted in?

Many thanks,
Shi
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

2017-06-07 Thread João Henriques

Higher complexity water models such as TIP5P and so on are able to better
reproduce bulk water properties (please check the paper I linked in my
earlier email). However, these models require more computational effort
(due to the increased number of interactions) and may not work well in
conjunction with a protein (many protein force fields were developed to be
used with specific water models). As Justin said, none of them gets
everything right.

/J

On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Justin,
> Thank you very much. I will try the possible water models.
>
>
> Do you know if there are water models to resemble frozen state?
>
>
> Yours sincerely
> Cheng
>
>
>
>
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Thu, Jun 8, 2017 00:50 AM
> To:  "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users" s.org_gmx-us...@maillist.sys.kth.se>;
>
> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Joao,
> Thank you for your help and the paper link.
>
>
> I was following Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/03_solvate.html
> On that page, it says "spc216.gro as the solvent configuration for SPC,
> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water)
> after the solvation step. So I assume "spc216.gro" refer to all the
> three-point water models?
>
>
> I am trying to see if my protein will be denatured in cold condition.
>
>
> Yours sincerely
> Cheng
>
>
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Wed, Jun 7, 2017 10:01 PM
> To:  "gromacs.org_gmx-users";
> Cc:  "ZHANG Cheng"<272699...@qq.com>;
> Subject:  Simulate protein at subzero condition in aqueous buffer
>
>
>
> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous
> buffer, to see if it becomes more stable than the elevated temperature
> (e.g. 65 C). Can I ask what is the valid temperature range for water
> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
> system as liquid state instead of frozen state? Thank you.
>
>
> Yours sincerely
> Cheng
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Justin,
Thank you very much. I will try the possible water models.


Do you know if there are water models to resemble frozen state?


Yours sincerely
Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Thu, Jun 8, 2017 00:50 AM
To:  "ZHANG Cheng"<272699...@qq.com>; 
"gromacs.org_gmx-users"; 

Subject:  Re: Simulate protein at subzero condition in aqueous buffer



Dear Joao,
Thank you for your help and the paper link.


I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, 
or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the 
solvation step. So I assume "spc216.gro" refer to all the three-point water 
models?


I am trying to see if my protein will be denatured in cold condition. 


Yours sincerely
Cheng


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Wed, Jun 7, 2017 10:01 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  Simulate protein at subzero condition in aqueous buffer



Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to 
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I 
ask what is the valid temperature range for water "spc216.gro" ? If I run the 
simulation at -40 C, does it still assume the system as liquid state instead of 
frozen state? Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

On 6/7/17 12:50 PM, ZHANG Cheng wrote:

Dear Joao,
Thank you for your help and the paper link.

I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P
water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I
assume "spc216.gro" refer to all the three-point water models?

It is as Joao has said - that's just a coordinate file of a pre-equilibrated box
of water that was generated using the SPC water model. You can indeed use it to
simulate other 3-point water model systems following an initial equilibration.

I am trying to see if my protein will be denatured in cold condition.

The properties of the water model are going to be critical here. For instance,
SPC has a maximum density around -41 C, which is obviously very unphysical
(water has a real maximum density at +4 C) so if you're seeking to model
behavior at -40 C, then SPC is a very bad choice because its properties are not
realistic. I suggest you investigate the many possible water models that exist
and find one or more that might reproduce some of the most important properties.
None of them gets everything right.

-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] Simulate protein at subzero condition in aqueous buffer

Dear Joao,
Thank you for your help and the paper link.


I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, 
or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the 
solvation step. So I assume "spc216.gro" refer to all the three-point water 
models?


I am trying to see if my protein will be denatured in cold condition. 


Yours sincerely
Cheng


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Wed, Jun 7, 2017 10:01 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  Simulate protein at subzero condition in aqueous buffer



Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to 
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I 
ask what is the valid temperature range for water "spc216.gro" ? If I run the 
simulation at -40 C, does it still assume the system as liquid state instead of 
frozen state? Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] RDF of a group around CNT axis

Dear Srinivas,
That's absolutely right, I want to calculate the RDF of a certain
group around the central axis of a nanotube.
And as I know that the RDF of the CNT around its axis is just a sharp peak
at the radius, I just tested the command-line parameters for this case, to
specify that which command-line should be used.

And honestly I do not understand the last sentence of your reply, could you
please specify that after isolating the desired group, what command-line I
should use?

Sincerely,
Sajjad



On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI <
scm...@scarletmail.rutgers.edu> wrote:

> If I understand you correctly: you want to calculate the RDF of a certain
> group (NOT part of the nanotube) around the central axis of a nanotube?
>
> The way I do these calculations is to use the gmx trjconv tool to isolate a
> trajectory file of ONLY the gropus I am interested in and run my
> calculations on that.
> If you expect to see one peak but see many that might mean that the RDF is
> picking up groups that you don't want it to.
>
> Hope that helps,
> Srinivas
>
> On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
> wrote:
>
> > Dear experts,
> > I want to calculate rdf of a certain group around the axis of a cnt, but
> I
> > do not know what are the proper parameters to choose in the command-line.
> > To test the parameters, I calculated the rdf of cnt itself around its
> axis
> > which must be a sharp peak at the cnt radius.
> > I tested the following: (both selection groups of reference and rdf are
> > CNT)
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
> > gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
> >
> > BUT all the results are the same!!! and surprisingly they have multiple
> > sharp peaks at different ranges, which I expected just one peak at the
> > radius of the CNT 
> > It is notable that the CNT is aligned to z axis.
> > (the first two peaks are listed below):
> >
> >   0.000 211939.438
> >   0.002 53771.996
> >   0.004 11278.401
> >   0.006 3935.633
> >   0.008 1782.280
> >   0.010  809.616
> >   0.012  584.723
> >   0.014  536.531
> >   0.016  292.361
> >   0.018  149.929
> >   0.020   94.455
> >   0.022   00.000
> >   ...
> >   ...
> >   ...
> >   0.11800.000
> >   0.1200.375
> >   0.1222.212
> >   0.1240.725
> >   0.1266.069
> >   0.128   36.545
> >   0.130  114.868
> >   0.132  278.390
> >   0.134 1669.916
> >   0.136 2360.069
> >   0.138  346.139
> >   0.140  183.770
> >   0.142   39.277
> >
> > Could you please explain to me that what should I do?
> > --
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Re: [gmx-users] mdp options in GROMACS 4.5.5




On 6/7/17 10:05 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Dear Mark,
I was using version 5.1.4, but I got this error when using "gmx mdrun":
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted

I tried version 5.0.4, too, and I got the same error. Hence, I decided to use 
the 4.5.5 version which does not give me that error.


If you're having a problem with a specific version, you should try something 
*newer* rather than significantly older.  Your posts about that issue went 
unresolved because there's not nearly enough information about what you did to 
install 5.1.4 (hardware, OS, compilers, your cmake command, etc).


Try with 2016.3 for something modern and actively being maintained.  It's a lot 
more effective for the developers to troubleshoot issues with the current 
version than one that is not even officially supported any more.


-Justin


Mohammad

   From: Mark Abraham 
  To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com
  Sent: Wednesday, 7 June 2017, 13:02:46
  Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5

Hi,You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-)Mark

On Tue, 6 Jun 2017 17:49 João Henriques  wrote:

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).

/J

On Tue, Jun 6, 2017 at 5:45 PM, João Henriques  wrote:


Hi All,
I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
used as input into grompp to generate em.tpr
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps
to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor
list and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor
list (simple, grid)
coulombtype = PME   ; Treatment of long range
electrostatic interactions
rcoulomb= 1.0   ; Short-range electrostatic
cut-off
rvdw= 1.0   ; Short-range Van der Waals
cut-off
pbc = xyz   ; Periodic Boundary Conditions
(yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
which said that the cutoff-scheme is not recognized. what should I write
instead of "cutoff-scheme" in this version?
Thanks,Mohammad
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--
==

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] Simulate protein at subzero condition in aqueous buffer

2017-06-07 Thread João Henriques

Hello,

"spc216.gro" is not a water model, it's just a pre-equilibrated simulation
box (300 K and 1 bar) with the coordinates of 216 3-site water molecules.
SPC and TIP3P are two examples of 3-site water models. Water model
properties are well studied and tabled (e.g.
http://aip.scitation.org/doi/10.1063/1.1862245).

I am no expert in pure water simulations, but I doubt 3-site water models
can reproduce ice in a realistic way. Will the force field even hold at
that temperature? I really don't understand why you'd want to try something
like this. However, and to finish, there's one thing I can tell you for
sure: your system will be much more "stable" at -40ºC. Why, because it will
barely move from it's initial conformation, due to the very low thermal
energy. In sum, you'll spend computational time sampling almost nothing.

Best regards,
João

On Wed, Jun 7, 2017 at 4:01 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous
> buffer, to see if it becomes more stable than the elevated temperature
> (e.g. 65 C). Can I ask what is the valid temperature range for water
> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the
> system as liquid state instead of frozen state? Thank you.
>
>
> Yours sincerely
> Cheng
> --
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Re: [gmx-users] RDF of a group around CNT axis

2017-06-07 Thread SRINIVAS MUSHNOORI

If I understand you correctly: you want to calculate the RDF of a certain
group (NOT part of the nanotube) around the central axis of a nanotube?

The way I do these calculations is to use the gmx trjconv tool to isolate a
trajectory file of ONLY the gropus I am interested in and run my
calculations on that.
If you expect to see one peak but see many that might mean that the RDF is
picking up groups that you don't want it to.

Hope that helps,
Srinivas

On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani 
wrote:

> Dear experts,
> I want to calculate rdf of a certain group around the axis of a cnt, but I
> do not know what are the proper parameters to choose in the command-line.
> To test the parameters, I calculated the rdf of cnt itself around its axis
> which must be a sharp peak at the cnt radius.
> I tested the following: (both selection groups of reference and rdf are
> CNT)
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
> gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com
>
> BUT all the results are the same!!! and surprisingly they have multiple
> sharp peaks at different ranges, which I expected just one peak at the
> radius of the CNT 
> It is notable that the CNT is aligned to z axis.
> (the first two peaks are listed below):
>
>   0.000 211939.438
>   0.002 53771.996
>   0.004 11278.401
>   0.006 3935.633
>   0.008 1782.280
>   0.010  809.616
>   0.012  584.723
>   0.014  536.531
>   0.016  292.361
>   0.018  149.929
>   0.020   94.455
>   0.022   00.000
>   ...
>   ...
>   ...
>   0.11800.000
>   0.1200.375
>   0.1222.212
>   0.1240.725
>   0.1266.069
>   0.128   36.545
>   0.130  114.868
>   0.132  278.390
>   0.134 1669.916
>   0.136 2360.069
>   0.138  346.139
>   0.140  183.770
>   0.142   39.277
>
> Could you please explain to me that what should I do?
> --
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Re: [gmx-users] mdp options in GROMACS 4.5.5

2017-06-07 Thread ‪Mohammad Roostaie‬ ‪

Dear Mark,
I was using version 5.1.4, but I got this error when using "gmx mdrun":
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted

I tried version 5.0.4, too, and I got the same error. Hence, I decided to use 
the 4.5.5 version which does not give me that error.
Mohammad

  From: Mark Abraham 
 To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com 
 Sent: Wednesday, 7 June 2017, 13:02:46
 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5

Hi,You almost certainly don't want to use version 4.5.5. It's many years old, 
slow and contains many bugs that have been fixed. Get a new version installed 
;-)Mark
On Tue, 6 Jun 2017 17:49 João Henriques  wrote:

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).

/J

On Tue, Jun 6, 2017 at 5:45 PM, João Henriques  wrote:

> Hi!
>
> I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> manual for that version (or the closest one).
>
> Cheers,
>
> /J
>
> On Tue, Jun 6, 2017 at 3:27 PM,  wrote:
>
>> Hi All,
>> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
>> used as input into grompp to generate em.tpr
>> integrator      = steep         ; Algorithm (steep = steepest descent
>> minimization)
>> emtol           = 1000.0        ; Stop minimization when the maximum
>> force < 1000.0 kJ/mol/nm
>> emstep      = 0.01      ; Energy step size
>> nsteps          = 5         ; Maximum number of (minimization) steps
>> to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist             = 1             ; Frequency to update the neighbor
>> list and long range forces
>> cutoff-scheme   = Verlet
>> ns_type             = grid              ; Method to determine neighbor
>> list (simple, grid)
>> coulombtype         = PME               ; Treatment of long range
>> electrostatic interactions
>> rcoulomb            = 1.0               ; Short-range electrostatic
>> cut-off
>> rvdw                = 1.0               ; Short-range Van der Waals
>> cut-off
>> pbc                     = xyz           ; Periodic Boundary Conditions
>> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
>> which said that the cutoff-scheme is not recognized. what should I write
>> instead of "cutoff-scheme" in this version?
>> Thanks,Mohammad
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[gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to 
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I 
ask what is the valid temperature range for water "spc216.gro" ? If I run the 
simulation at -40 C, does it still assume the system as liquid state instead of 
frozen state? Thank you.


Yours sincerely
Cheng
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[gmx-users] Doubt about Normal Mode Analysis while scaling nonbonded interactions

2017-06-07 Thread Varvdekar Bhagyesh Rajendra

Dear all,

Is there any way of scaling the Coulombic and/or van der Waals interactions 
between a protein-ligand system and simultaneously doing Normal Mode analysis 
on the perturbed system while scaling, perhaps using free-energy code in 
Gromacs?

Thanking in anticipation,

Best Regards,

Bhagyesh
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[gmx-users] RDF of a group around CNT axis

Dear experts,
I want to calculate rdf of a certain group around the axis of a cnt, but I
do not know what are the proper parameters to choose in the command-line.
To test the parameters, I calculated the rdf of cnt itself around its axis
which must be a sharp peak at the cnt radius.
I tested the following: (both selection groups of reference and rdf are CNT)
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos mol_com
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos res_com
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_res_com
gmx rdf -f md.gro -s md.tpr  -o trdf.xvg -xy -selrpos whole_mol_com

BUT all the results are the same!!! and surprisingly they have multiple
sharp peaks at different ranges, which I expected just one peak at the
radius of the CNT 
It is notable that the CNT is aligned to z axis.
(the first two peaks are listed below):

  0.000 211939.438
  0.002 53771.996
  0.004 11278.401
  0.006 3935.633
  0.008 1782.280
  0.010  809.616
  0.012  584.723
  0.014  536.531
  0.016  292.361
  0.018  149.929
  0.020   94.455
  0.022   00.000
  ...
  ...
  ...
  0.11800.000
  0.1200.375
  0.1222.212
  0.1240.725
  0.1266.069
  0.128   36.545
  0.130  114.868
  0.132  278.390
  0.134 1669.916
  0.136 2360.069
  0.138  346.139
  0.140  183.770
  0.142   39.277

Could you please explain to me that what should I do?
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Re: [gmx-users] Gromacs




On 6/7/17 8:36 AM, saranya wrote:

I have already done simulation for protein and drug interacted protein
complexes for 100ns. I just checked out the pressure of my system by using
gmx energy command, but the calculated pressure is quite altered (20,000
pressure bar).
Moreover, when I calculated the temperature of my system, the result was
zero. I am not able to understand the origin of this discrepancy. kindly
consider the above issue and please help me out.



How are you calculating these properties?  Is this directly the output from gmx 
energy?  What were your .mdp settings?


-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] mdrun with multi option

2017-06-07 Thread Debdip Bhandary


Thank you Mark.

Let me explain my scenario here - Umbrella sampling simulations with 15 
windows are run using -multi option to obtain PMFs. I have not noticed 
any issues with the output files (trr, pullf etc.) yet. I have carried 
out WHAM analysis using gmx wham option and obtained smooth PMFs. Please 
explain me in which way 'gmx mdrun -multi' option may lead to less 
reliable with output file and how I can be sure of it.


Thanks again.
regards,
Debdip

On 07.06.2017 12:39, Mark Abraham wrote:

Hi,

gmx mdrun -multidir is a good way to run a group of similar but otherwise
uncoupled simulations - they remain uncoupled unless you choose something
that couples them, such as replica exchange. gmx mdrun -multi is a bit less
reliable with output files.

Mark

On Wed, Jun 7, 2017 at 12:34 PM Debdip Bhandary <
debdip.bhand...@mv.uni-kl.de> wrote:


Dear Users,

I have doubts regarding simulating multiple systems using mdrun '-multi'
option.

I have seen that people have used this option for replica exchange (with
'-replex' option, of course) where information are exchanged between the
systems. In case of different systems (such as different windows in
Umbrella sampling simulations, liquid water systems at different
temperatures, etc.), as per my understanding (from user manual), there
is no exchange of information between the systems and simulations are
run without any influence of each other. Am I correct here? or is there
any issue when different systems are simulated using -multi/multidir
options? Any information regarding this would be appreciated.

Thank you in advance.

Best regards,
Debdip Bhandary

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[gmx-users] 3-10 or Pi helices are changing to Alpha over the time: 100 ns MD

2017-06-07 Thread prasun kumar

Hi Group

I have been trying to run a simulation that contains both 3-10 and alpha
helical peptides.

I am using "AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et
al., Proteins 78, 1950-58, 2010)" forcefield.

Over the course of simulation, the 3-10 helix is changing to alpha as
suggested by do_dssp (I am using the newer version of DSSP).

Thanx in advance for the help.

Regards
Prasun
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success
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Re: [gmx-users] number of coordinates does not match after POSRES

2017-06-07 Thread Simon Kit Sang Chu

Hi Mark,

I think I solved the problem. It should be DPOSRES instead of POSRES. The
define command should be implemented as "define = -DPOSRES". Finally, the
chainX_porse.itp should be included in the master topology file, not
chainX-pace.top.

Thanks again by the way.

Simon

2017-06-07 19:18 GMT+08:00 Simon Kit Sang Chu :

> Hi Mark,
>
> Thanks for your prompt reply. What surprises me is that a change of
> "define = POSRES" could cause a problem. The full output from grompp is -
>
> checking input for internal consistency...
> calling cpp...
> cpp: error: POSRES: No such file or directory
> cpp: warning: ‘-x c’ after last input file has no effect
> cpp: fatal error: no input files
> compilation terminated.
> cpp exit code: 1024
> Tried to execute: 'cpp  -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top
> POSRES p1p2.top > gromppDTyNuM'
> The 'cpp' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> ---
> Program grompp, VERSION 3.3.1
> Source code file: grompp.c, line: 448
>
> Fatal error:
> number of coordinates in coordinate file (npt.gro, 74787)
>  does not match topology (p1p2.top, 0)
>
>
> The additional information is attached here as a reference.
>
> *chainA-pace.top*
> [ moleculetype ]
> ; Namenrexcl
> Protein_A   3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
>chargeB  massB
>  1 N+  1MET  N  10.7 17   ;
> qtot 0.7
> .
> .
> .
>   919   922   921   920 20.0  300.0
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "chainA_posre.itp"
> #endif
>
>
> *chainA_porse.itp*
> ; position restraints for r_1-62_&_Backbone of FullP1P2 in water
>
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> .
> .
> .
>  5231   1000   1000   1000
>  5301   1000   1000   1000
>
> Simon
>
>
> 2017-06-07 16:28 GMT+08:00 Mark Abraham :
>
>> Hi,
>>
>> We can't tell, because position restraints are an attribute of
>> moleculetypes and those are hidden in your itp files and you didn't share
>> which moleculetype grompp reported was the problem. Please copy and paste
>> terminal output to make a useful description.
>>
>> You'll need to include the position restraint file appropriate to each
>> moleculetype, of course - not the same one each time.
>>
>> Mark
>>
>> On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu 
>> wrote:
>>
>> > Hi,
>> >
>> > Initially, my topology file can run grompp with .mdp and .gro. However,
>> > after putting POSRES in my mdp, the warning "number of coordinates does
>> not
>> > match" and there is no coordinate recognized in my topology file
>> anymore.
>> > Therefore, the option POSRES somehow changes everything.
>> >
>> > The topology file is put here. Is there anything I have written
>> > incorrectly?
>> >
>> > ; Include forcefield parameters
>> > #include "ffPACE_1.3.itp"
>> >
>> > ; Include chain topologies
>> > #include "chainA-pace.top"
>> > #include "chainB-pace.top"
>> >
>> > ; Include water topology
>> > #include "cgWater.itp"
>> >
>> > ; Include topology for ions
>> > #include "martini_v2.0_ions.itp"
>> >
>> > [ system ]
>> > ; Name
>> > FullP1P2 in water
>> >
>> > [ molecules ]
>> > ; Compound#mols
>> > Protein_A 1
>> > Protein_B 1`
>> > SOL 72899
>> > NA+ 20
>> > --
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Re: [gmx-users] RMSD analysis




On 6/6/17 4:01 PM, RAHUL SURESH wrote:

Dear Justin

I think I have confused so much.
Let me try to put it in simple way.

1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of
monomer(just protein) to explain stability?



RMSD may be an indicator of something going on but by itself is useless.

Rg is only useful if the protein undergoes a large structural change or 
unfolding.

RMSF can be useful if the ensembles are converged; it is subject to big 
variation if you have any non-equilibrium sampling.



2. Time step of monomer(just protein) simulation is 150ns and
protein-ligand complex is 50ns. In this case is it valid to compare the
above analyses between monomer and complex?


Compare like with like.  I wouldn't believe comparisons between single 
trajectories of differing lengths have any meaning.


-Justin



Dear Justin I apologise if I am not to your mark to explain in better way.




On Wed, 7 Jun 2017 at 1:19 AM, Justin Lemkul  wrote:




On 6/6/17 1:11 PM, RAHUL SURESH wrote:

Dear Justin

Thank you. I am considering  Rmsd rmsf rg as just supplementary analysis
for my study.  My aim to analyse  conformational change in protein. I

would

like to bring a note on protein stability after ligand binding. I don't
know to which part of monomer I can compare the rmsd of complex with.
First 50ns or last .. can you please help me with this?


I'm not following.  You're talking about monomers and time intervals as if
they're interchangeable.  What's the story?  Do you have a multimer?  Are
you
curious about demonstrating convergence?

-Justin


On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul  wrote:




On 6/6/17 2:12 AM, RAHUL SURESH wrote:

Dear Users

*Exp procedure:*
I have simulated the protein monomer for 150ns. Using the 150ns

conformer,

ligand is docked to the protein using autodock and the simulation is
carried out for 50ns.

*Analysis:*

Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
with that of monomer? If yes which part of the monomer trajectory

should

be

considered.?



This is up to you to determine in light of whatever your goals are in
running
the simulation.  What are you trying to test or determine?  Unless the
protein's
stability is seriously impacted by the ligand, RMSD and Rg are useless.
RMSF
might be useful if there are motions that are amplified or damped by

ligand

binding.  Run the analysis and see what happens on a per-residue basis.

-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

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==

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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

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==

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

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Re: [gmx-users] number of coordinates does not match after POSRES




On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote:

Hi Mark,

Thanks for your prompt reply. What surprises me is that a change of "define
= POSRES" could cause a problem. The full output from grompp is -

checking input for internal consistency...
calling cpp...
cpp: error: POSRES: No such file or directory


Well, here's the first problem.  Your syntax is incorrect (#ifdef keywords are 
prefixed with -D, so "define = POSRES" does nothing but "define = -DPOSRES" 
would invoke position restraints.



cpp: warning: ‘-x c’ after last input file has no effect
cpp: fatal error: no input files
compilation terminated.
cpp exit code: 1024
Tried to execute: 'cpp  -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top
POSRES p1p2.top > gromppDTyNuM'
The 'cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
---
Program grompp, VERSION 3.3.1


Is there a reason you are using prehistoric, deprecated software?


Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (npt.gro, 74787)
  does not match topology (p1p2.top, 0)



This suggests mangled syntax, so check for typos, bad line endings, etc. and use 
a more modern GROMACS version.


-Justin



The additional information is attached here as a reference.

*chainA-pace.top*
[ moleculetype ]
; Namenrexcl
Protein_A   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
  1 N+  1MET  N  10.7 17   ;
qtot 0.7
.
.
.
   919   922   921   920 20.0  300.0

; Include Position restraint file
#ifdef POSRES
#include "chainA_posre.itp"
#endif


*chainA_porse.itp*
; position restraints for r_1-62_&_Backbone of FullP1P2 in water

[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
.
.
.
  5231   1000   1000   1000
  5301   1000   1000   1000

Simon


2017-06-07 16:28 GMT+08:00 Mark Abraham :


Hi,

We can't tell, because position restraints are an attribute of
moleculetypes and those are hidden in your itp files and you didn't share
which moleculetype grompp reported was the problem. Please copy and paste
terminal output to make a useful description.

You'll need to include the position restraint file appropriate to each
moleculetype, of course - not the same one each time.

Mark

On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu 
wrote:


Hi,

Initially, my topology file can run grompp with .mdp and .gro. However,
after putting POSRES in my mdp, the warning "number of coordinates does

not

match" and there is no coordinate recognized in my topology file anymore.
Therefore, the option POSRES somehow changes everything.

The topology file is put here. Is there anything I have written
incorrectly?

; Include forcefield parameters
#include "ffPACE_1.3.itp"

; Include chain topologies
#include "chainA-pace.top"
#include "chainB-pace.top"

; Include water topology
#include "cgWater.itp"

; Include topology for ions
#include "martini_v2.0_ions.itp"

[ system ]
; Name
FullP1P2 in water

[ molecules ]
; Compound#mols
Protein_A 1
Protein_B 1`
SOL 72899
NA+ 20
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--
==

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
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[gmx-users] mdrun with multi option

2017-06-07 Thread Debdip Bhandary


Dear Users,

I have doubts regarding simulating multiple systems using mdrun '-multi' 
option.


I have seen that people have used this option for replica exchange (with 
'-replex' option, of course) where information are exchanged between the 
systems. In case of different systems (such as different windows in 
Umbrella sampling simulations, liquid water systems at different 
temperatures, etc.), as per my understanding (from user manual), there 
is no exchange of information between the systems and simulations are 
run without any influence of each other. Am I correct here? or is there 
any issue when different systems are simulated using -multi/multidir 
options? Any information regarding this would be appreciated.


Thank you in advance.

Best regards,
Debdip Bhandary


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Re: [gmx-users] Ramachandran plot

Hi,

This is why you should actually copy and paste your command lines so you
don't waste your time ;-) And mine.

Unless you wrote your entire system to your xtc file, your tpr has more
atoms than your xtc, and thus probably some more dihedrals. Make a matching
subset of your tpr using gmx convert-tpr, and use that with gmx rama -s.

Mark

On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH 
wrote:

> Dear Mark
> Thank you
>
> gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg
>
> This was my command..
>
> I didn't choose any dihedral particularly
>
>
> On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Sounds like your choice of dihedrals doesn't match your system. How did
> you
> > select them?
> >
> > Mark
> >
> > On Wed, 7 Jun 2017 08:41 RAHUL SURESH  wrote:
> >
> > > Dear Users
> > >
> > > When I try to execute ramachandran plot analysis, I get the following
> > note
> > > like "Dihedral around 5809,5816 not found in topology. Using mult=3"
> > > (nearly 30-40 dihedrals). What is it about?
> > >
> > > Input is just protein structure extended upto 150ns.
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
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Re: [gmx-users] Ramachandran plot

2017-06-07 Thread RAHUL SURESH

Dear Mark
Thank you

gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg

This was my command..

I didn't choose any dihedral particularly


On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham 
wrote:

> Hi,
>
> Sounds like your choice of dihedrals doesn't match your system. How did you
> select them?
>
> Mark
>
> On Wed, 7 Jun 2017 08:41 RAHUL SURESH  wrote:
>
> > Dear Users
> >
> > When I try to execute ramachandran plot analysis, I get the following
> note
> > like "Dihedral around 5809,5816 not found in topology. Using mult=3"
> > (nearly 30-40 dihedrals). What is it about?
> >
> > Input is just protein structure extended upto 150ns.
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Simulation of pure water

Hi,

On Wed, 7 Jun 2017 06:37 G R  wrote:

> Dear all,
>
> I want to calculate the relaxation of pure water cell at room temperature
> and at freezing point, monitoring its equilibration in volume and in
> potential energy. I have 3 question: 1) Can I use packmol for my initial
> configuration?

Maybe, I don't know. gmx solvate works.

if there is any other option,please tell me. 2) Can I use
> easily pdb2gmx to generate the topology file?

Not really, it's designed for solute in water systems. But you can take any
such topology and remove the solute moleculetype and subsections.

3) Which Forcefield is better
> for this calculation?
>

You're not really going to use what is commonly called a force field, but
just a water model. There's lots of them, and you should choose one that
has been shown to be useful for your kind of study. That's the science
part, and your job ;-)

Mark

I'v already read some tutorial, but if you have any suggestion it woulb be
> appreciated.
>
> Thank you in advance
>  GR
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Re: [gmx-users] RMSD Matrix Error

Hi,

You might want to measure the autocorrelation time of RMSD from your
reference structure. Then you'll have an idea how long you have to wait to
make a statistically independent observation.

Mark

On Tue, 6 Jun 2017 08:25 Apramita Chand  wrote:

> Dear Mark,
> Thanks for your reply. I think you're right about the space needed for
> generating RMSD Matrix. I definitely was short of 160GB !!
> Further, you've talked about me using highly correlated frames and that a
> suitable sub-sampling might solve the problem. How would I know which
> frames to use?
>
>
>
> Message: 2
> Date: Mon, 05 Jun 2017 01:37:37 +
> From: Mark Abraham 
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] RMSD Matrix error
> Message-ID:
>

Re: [gmx-users] mdp options in GROMACS 4.5.5

Hi,

You almost certainly don't want to use version 4.5.5. It's many years old,
slow and contains many bugs that have been fixed. Get a new version
installed ;-)

Mark

On Tue, 6 Jun 2017 17:49 João Henriques 
wrote:

> Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
> mean, not the integration).
>
> /J
>
> On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <
> joao.m.a.henriq...@gmail.com
> > wrote:
>
> > Hi!
> >
> > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> > manual for that version (or the closest one).
> >
> > Cheers,
> >
> > /J
> >
> > On Tue, Jun 6, 2017 at 3:27 PM,  wrote:
> >
> >> Hi All,
> >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
> >> used as input into grompp to generate em.tpr
> >> integrator  = steep ; Algorithm (steep = steepest descent
> >> minimization)
> >> emtol   = 1000.0; Stop minimization when the maximum
> >> force < 1000.0 kJ/mol/nm
> >> emstep  = 0.01  ; Energy step size
> >> nsteps  = 5 ; Maximum number of (minimization) steps
> >> to perform
> >>
> >> ; Parameters describing how to find the neighbors of each atom and how
> to
> >> calculate the interactions
> >> nstlist = 1 ; Frequency to update the neighbor
> >> list and long range forces
> >> cutoff-scheme   = Verlet
> >> ns_type = grid  ; Method to determine neighbor
> >> list (simple, grid)
> >> coulombtype = PME   ; Treatment of long range
> >> electrostatic interactions
> >> rcoulomb= 1.0   ; Short-range electrostatic
> >> cut-off
> >> rvdw= 1.0   ; Short-range Van der Waals
> >> cut-off
> >> pbc = xyz   ; Periodic Boundary Conditions
> >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the
> error
> >> which said that the cutoff-scheme is not recognized. what should I write
> >> instead of "cutoff-scheme" in this version?
> >> Thanks,Mohammad
> >> --
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> >
> >
> >
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Re: [gmx-users] Energy Minimisation

Hi,

Please read the advice on system preparation on the GROMACS webpage. You
probably have clashing atoms or missing atoms (check all the warnings!)

Mark

On Tue, 6 Jun 2017 20:19 Pandya, Akash  wrote:

> Hi all,
>
> I have used the steepest descent method to minimise my system. It kept
> saying certain water molecules could not be settled but it still managed to
> reached the maximum force. Then I used the Conjugate gradient method and I
> get this error message. Can someday please tell me how I would check and
> ultimately get rid of the bad contacts.
>
> Fatal error:
> The coordinates could not be constrained. Minimizer 'cg' can not handle
> constraint failures, use minimizer 'steep' before using 'cg'.
>
>
>
> Akash
>
>
>
>
>
>
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Re: [gmx-users] Ramachandran plot

Hi,

Sounds like your choice of dihedrals doesn't match your system. How did you
select them?

Mark

On Wed, 7 Jun 2017 08:41 RAHUL SURESH  wrote:

> Dear Users
>
> When I try to execute ramachandran plot analysis, I get the following note
> like "Dihedral around 5809,5816 not found in topology. Using mult=3"
> (nearly 30-40 dihedrals). What is it about?
>
> Input is just protein structure extended upto 150ns.
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] number of coordinates does not match after POSRES