date:20160415

Re: [gmx-users] what is the source of "CHL1" cholesterol in the gromacs charmm port?

2016-04-15 Thread Christopher Neale

Thank you very much Justin!

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 15 April 2016 05:46
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] what is the source of "CHL1" cholesterol in the 
gromacs charmm port?

On 4/15/16 1:29 AM, Christopher Neale wrote:
>
> Dear Users:
>
> When I look at charmm36-jun2015.ff/merged.rtp downloaded from
> http://mackerell.umaryland.edu/charmm_ff.shtml , it has a cholesterol
> molecule named CHL1. However, I do not find such a molecule in the
> charmm-specific toppar_c36_feb16.tgz downloaded from the same site. In the

Just a note to everyone: as the dates should make very obvious, the Feb 2016
release of the CHARMM force field is much newer than the port; you should not
expect exact agreement between these files.  I have not yet made an updated
port, but it's on my to-do list.

> later tarball, I do find cholestrol as "RESI CLOL" in top_all36_cgenff.rtf
> but that is from cgenff and the values differ. As a simple proof of the
> difference, the charge on O3 is not the same, though the differences extend
> beyond that.
>
> Some comments in the charmm-format files refer to
> toppar_all27_lipid_cholesterol.str , but I can not find that file ... I
> checked in toppar_c31b1.tar.gz from the same website but to no avail.
>
> So my question is what is the source for CHL1 in
> charmm36-jun2015.ff/merged.rtp ?
>

toppar/stream/lipid/toppar_all36_lipid_cholesterol.str

Many residues come from the stream files (either from residues found there or
created from patches therein).

-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] Effect of bond constraints on equilibrium densities of equilibrated liquids

2016-04-15 Thread Miguel Caro

Apologies, the graph didn't show up. It can be viewed here:

mcaroba.dyndns.org/misc/wat_ace.png

Miguel

On 2016-04-15 18:51, Miguel Caro wrote:
> Hi all,
>
> I am running some test calculations with acetonitrile/water mixtures
> using the GAFF topologies as available from virtualchemistry.org (by the
> way, thanks for this great resource). I obtain equilibrium densities
> from averages over different independent configurations after 1 ns
> equilibration periods (298 K, 1 bar, 400 water molecules and 200
> acetonitrile molecules at the end points). The equilibrium density I
> obtain for pure acetonitrile is larger than that reported on the website
> for GAFF
> (http://virtualchemistry.org/molecule.php?filename=acetonitrile.zmat)
> and slightly closer to the experimental value of 0.78 g/cm^3: it is
> about 0.8 g/cm^3 for me compared to 0.73 g/cm^3 from the reference
> calculation. I hope the graph copy-pasted below shows up on my email, to
> help illustrate the issue (each data point is one configuration
> equilibrated for 1ns). Going to the JCTC paper referenced on the website
> (Caleman et al. JCTC 8, 61 [2012]), it appears unless I'm mistaken that
> the reference results were obtained with constrained bonds (Table 1 on
> that paper, "LIQ" item). However, I am allowing all bonds to vibrate in
> my simulation (with appropriate small time steps).
>
> My question is whether I can/should expect the difference in predicted
> density to originate from the lifted bond constraints, or is there
> something else flawed about how I'm running this simulation. I.e.,
> should I run longer simulations, calculate for each configuration the
> average density over the simulated trajectory instead of taking the
> final density value, etc.?
>
> Many thanks for you help,
> Miguel
>
>

-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcar...@gmail.com*
Work: *miguel.c...@aalto.fi*
Website: http://mcaroba.dyndns.org
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[gmx-users] Effect of bond constraints on equilibrium densities of equilibrated liquids

2016-04-15 Thread Miguel Caro

Hi all,

I am running some test calculations with acetonitrile/water mixtures
using the GAFF topologies as available from virtualchemistry.org (by the
way, thanks for this great resource). I obtain equilibrium densities
from averages over different independent configurations after 1 ns
equilibration periods (298 K, 1 bar, 400 water molecules and 200
acetonitrile molecules at the end points). The equilibrium density I
obtain for pure acetonitrile is larger than that reported on the website
for GAFF
(http://virtualchemistry.org/molecule.php?filename=acetonitrile.zmat)
and slightly closer to the experimental value of 0.78 g/cm^3: it is
about 0.8 g/cm^3 for me compared to 0.73 g/cm^3 from the reference
calculation. I hope the graph copy-pasted below shows up on my email, to
help illustrate the issue (each data point is one configuration
equilibrated for 1ns). Going to the JCTC paper referenced on the website
(Caleman et al. JCTC 8, 61 [2012]), it appears unless I'm mistaken that
the reference results were obtained with constrained bonds (Table 1 on
that paper, "LIQ" item). However, I am allowing all bonds to vibrate in
my simulation (with appropriate small time steps).

My question is whether I can/should expect the difference in predicted
density to originate from the lifted bond constraints, or is there
something else flawed about how I'm running this simulation. I.e.,
should I run longer simulations, calculate for each configuration the
average density over the simulated trajectory instead of taking the
final density value, etc.?

Many thanks for you help,
Miguel


-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcar...@gmail.com*
Work: *miguel.c...@aalto.fi*
Website: http://mcaroba.dyndns.org
-- 
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Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs

2016-04-15 Thread Mark Abraham

Hi,

On Fri, Apr 15, 2016 at 3:44 PM Brett  wrote:

> Dear Mark,
>
>
>
> My protein was a 6-identical subunit protein complex, initially each
> subunit contains a ligand. I want to see the conformational change from
> ligand bond to ligand free state, during this process there were reports
> that significant conformation change would occur
>
>
> First from the initial PDB with the ligands, I delete the ligands and get
> the apo pdb, after pdb2gmx etc, I process the energy minimization, nvt
> equilibration and npt equilibration, then I start the production md. During
> the initial 6 ns production md, there were some conformation change
> observed, but I do not know whether it diffuse.
>

You also have a large number of water molecules. The outermost extent of
their shape (their "envelope") was what you observed as becoming more
spherical, once you required their representation to avoid jumps over the
duration of the trajectory.

In addition, I do not understand what is "the envelope of the diffusion",


If you do a large number of one-dimensional random walks, you have a
characteristic distribution of the results, right? Here, your water
molecules are doing a three-dimensional random walk, without jumps. The
distribution of their final displacements isn't going to resemble your
starting shape. But if you choose a representation where they jump, then
the starting shape will remain.

and does diffusion leads the box from cubic to sphere?
>

Don't confuse the representation with what happened. You told mdrun to do a
periodic simulation. If you later require the representation of the
trajectory to not have jumps over boundaries, you aren't changing the
simulation.

Mark

Brett
>
>
>
>
>
>
>
>
>
> At 2016-04-15 21:30:12, "Mark Abraham"  wrote:
> >Hi,
> >
> >On Fri, Apr 15, 2016 at 3:18 PM Brett  wrote:
> >
> >> Dear All,
> >>
> >> By xmgrace I have checked the xmgrace, I find the spike was between
> >> -8.245e+06 and -8.225e+06, is the spike massive or not?
> >>
> >>
> >> In addition, by
> >> gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc
> >> nojump -dump 6000,
> >>
> >>
> >> I got the 6 ns with water pdb and I have checked the pdb (with water
> box),
> >> I find the resi 366-367 were not disconnected!
> >>
> >>
> >> However, by gmx editconf, the original water box was in cubic, after
> "gmx
> >> trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump
> >> -dump 6000", the cubic water box was replaced by a rough sphere water
> box
> >> with the protein roughly in the center. Will you please explain why the
> >> cubic water box was replaced by the round sphere water box? Anything
> wrong
> >> I have made?
> >>
> >
> >You've simulated a bunch of molecules that diffuse. What shape would you
> >expect for the envelope of the diffusion? How would it vary over time?
> >
> >Further, by visual check if in a production MD I did not see residue
> >> disconnection caused by "Periodic_Boundary_Conditions", can we
> guarantee no
> >> minor disconnection occurred during the md (or significant bond length
> >> variance unobservable by the naked eye with pymol) if we did not process
> >> the trjconv correction step?
> >>
> >
> >The forces produced by such a disconnection would blow everything up
> >immediately. Since it didn't...
> >
> >Mark
> >
> >
> >> I am looking forward to getting a reply from you.
> >>
> >>
> >> Brett
> >>
> >>
> >>
> >>
> >>
> >>
> >> At 2016-04-14 20:02:43, "Mark Abraham" 
> wrote:
> >> >Hi,
> >> >
> >> >If this "separation" was real, would you have expected to see
> >> >
> >> >a) a massive spike in the potential energy
> >> >b) complete inability for the constraint algorithm to enforce bond
> >> lengths?
> >> >
> >> >Hint, you haven't seen that.
> >> >
> >> >Mark
> >> >
> >> >On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul 
> wrote:
> >> >
> >> >>
> >> >>
> >> >> On 4/14/16 5:35 AM, Brett wrote:
> >> >> > Dear All,
> >> >> >
> >> >> >
> >> >> >
> >> >> > Thanks the reply.
> >> >> >
> >> >> >
> >> >> > But I think I need to discuss with you further on whether I need to
> >> >> discontinue my production MD. As I mentioned, resi 366-367 separated
> >> from
> >> >> the major body of the protein. By pymol I find resi 366-367 were at
> one
> >> >> edge of the box and were almost outside of the water box, and its
> >> >> neighbouring residues resi 365 and resi 368 were at the opposite
> edge of
> >> >> the box and were also almost outside of the water box.
> >> >> >
> >> >> >
> >> >> > It seems that way, although at the initial step by editconf I have
> put
> >> >> the protein in the center of the cubic box (1.5 nm), during the
> first 6
> >> ns
> >> >> the protein has moved significantly in the box, and at some moment
> resi
> >> >> 366-367 have moved out of the box, leading to the disconnection of
> resi
> >> >> 366-367 from the major body of the protein and finally leading to
> resi
> >> >> 366-367 at the opposite of  its neighbouring residues resi 365 and
> resi
> >>

Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs

2016-04-15 Thread Brett

Dear Mark,



My protein was a 6-identical subunit protein complex, initially each subunit 
contains a ligand. I want to see the conformational change from ligand bond to 
ligand free state, during this process there were reports that significant 
conformation change would occur


First from the initial PDB with the ligands, I delete the ligands and get the 
apo pdb, after pdb2gmx etc, I process the energy minimization, nvt 
equilibration and npt equilibration, then I start the production md. During the 
initial 6 ns production md, there were some conformation change observed, but I 
do not know whether it diffuse.


In addition, I do not understand what is "the envelope of the diffusion", and 
does diffusion leads the box from cubic to sphere?


Brett









At 2016-04-15 21:30:12, "Mark Abraham"  wrote:
>Hi,
>
>On Fri, Apr 15, 2016 at 3:18 PM Brett  wrote:
>
>> Dear All,
>>
>> By xmgrace I have checked the xmgrace, I find the spike was between
>> -8.245e+06 and -8.225e+06, is the spike massive or not?
>>
>>
>> In addition, by
>> gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc
>> nojump -dump 6000,
>>
>>
>> I got the 6 ns with water pdb and I have checked the pdb (with water box),
>> I find the resi 366-367 were not disconnected!
>>
>>
>> However, by gmx editconf, the original water box was in cubic, after "gmx
>> trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump
>> -dump 6000", the cubic water box was replaced by a rough sphere water box
>> with the protein roughly in the center. Will you please explain why the
>> cubic water box was replaced by the round sphere water box? Anything wrong
>> I have made?
>>
>
>You've simulated a bunch of molecules that diffuse. What shape would you
>expect for the envelope of the diffusion? How would it vary over time?
>
>Further, by visual check if in a production MD I did not see residue
>> disconnection caused by "Periodic_Boundary_Conditions", can we guarantee no
>> minor disconnection occurred during the md (or significant bond length
>> variance unobservable by the naked eye with pymol) if we did not process
>> the trjconv correction step?
>>
>
>The forces produced by such a disconnection would blow everything up
>immediately. Since it didn't...
>
>Mark
>
>
>> I am looking forward to getting a reply from you.
>>
>>
>> Brett
>>
>>
>>
>>
>>
>>
>> At 2016-04-14 20:02:43, "Mark Abraham"  wrote:
>> >Hi,
>> >
>> >If this "separation" was real, would you have expected to see
>> >
>> >a) a massive spike in the potential energy
>> >b) complete inability for the constraint algorithm to enforce bond
>> lengths?
>> >
>> >Hint, you haven't seen that.
>> >
>> >Mark
>> >
>> >On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul  wrote:
>> >
>> >>
>> >>
>> >> On 4/14/16 5:35 AM, Brett wrote:
>> >> > Dear All,
>> >> >
>> >> >
>> >> >
>> >> > Thanks the reply.
>> >> >
>> >> >
>> >> > But I think I need to discuss with you further on whether I need to
>> >> discontinue my production MD. As I mentioned, resi 366-367 separated
>> from
>> >> the major body of the protein. By pymol I find resi 366-367 were at one
>> >> edge of the box and were almost outside of the water box, and its
>> >> neighbouring residues resi 365 and resi 368 were at the opposite edge of
>> >> the box and were also almost outside of the water box.
>> >> >
>> >> >
>> >> > It seems that way, although at the initial step by editconf I have put
>> >> the protein in the center of the cubic box (1.5 nm), during the first 6
>> ns
>> >> the protein has moved significantly in the box, and at some moment resi
>> >> 366-367 have moved out of the box, leading to the disconnection of resi
>> >> 366-367 from the major body of the protein and finally leading to resi
>> >> 366-367 at the opposite of  its neighbouring residues resi 365 and resi
>> 368
>> >> in the cubix box.
>> >> >
>> >> >
>> >> > Am I right?
>> >> >
>> >>
>> >> Diffusion is normal.  The residues are not actually disconnected.  You
>> can
>> >> use
>> >> trjconv to "fix" this state, but there is nothing physically wrong with
>> it.
>> >> mdrun cares about physics, not our visualization convenience.
>> >>
>> >> -Justin
>> >>
>> >> >
>> >> > Brett
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > At 2016-04-14 16:31:20, "Mark Abraham" 
>> wrote:
>> >> >> Hi,
>> >> >>
>> >> >> As the link Justin gave you says, and Tsjerk has since confirmed,
>> this
>> >> is
>> >> >> normal. There are infinitely many equivalent representations of your
>> >> >> simulation, not all of which will look connected for the thing that
>> is
>> >> of
>> >> >> interest.
>> >> >>
>> >> >> Strategies for handling visualisation are also on that link, but you
>> >> don't
>> >> >> need to handle anything within the simulation.
>> >> >>
>> >> >> Mark
>> >> >>
>> >> >> On Thu, 14 Apr 2016 09:48 Brett  wrote:
>> >> >>
>> >> >>> Dear All,
>> >> >>>
>> >> >>> As I have introduced in my previous e-mail,
>> >> >>>
>> >> >>> "After energy

[gmx-users] MARTINI simulation of protein-protein recognition

2016-04-15 Thread James Starlight

Dear Gromacs users!

I am looking for some tutorial for the MARTINI simulation of
protein-protein recognition dealing with the big membrane protein
simulated within the membrane and its assosiation with the small water
soluble protein. The question - is it possible in existing Martini
system conisdted of only membrane protein solvated in membrane with
water to
i) increase box size on Z
ii)add some water
iii) put another water soluble protein in new space (on the distance
of the initial membrane protein complex)
iv) edit topology of new system and run new md

assuming that i,ii and iv are trivial the problem here is the iii step :-)

or alternatively if I would like to run new simulation with those 2
proteins (in the unbound form) how I can prepare such complex system
consisted of big protein in membrane plus water soluble protein
unbound from it?

Thanks!

Gleb
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Re: [gmx-users] (no subject)

2016-04-15 Thread Mark Abraham

Hi,

Please see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Fri, Apr 15, 2016 at 12:22 PM ali osouli  wrote:

> Dear all
> My MD run movie shows that my ligand jump out of protein in the early
> picoseconds of simulation, does anybody knwos which step of my MD should i
> check?
> In additon to rutin steps i have included a distance restraint file to
> topolgy.itp.
> Best regards Ali
> --
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Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs

2016-04-15 Thread Mark Abraham

Hi,

On Fri, Apr 15, 2016 at 3:18 PM Brett  wrote:

> Dear All,
>
> By xmgrace I have checked the xmgrace, I find the spike was between
> -8.245e+06 and -8.225e+06, is the spike massive or not?
>
>
> In addition, by
> gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc
> nojump -dump 6000,
>
>
> I got the 6 ns with water pdb and I have checked the pdb (with water box),
> I find the resi 366-367 were not disconnected!
>
>
> However, by gmx editconf, the original water box was in cubic, after "gmx
> trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump
> -dump 6000", the cubic water box was replaced by a rough sphere water box
> with the protein roughly in the center. Will you please explain why the
> cubic water box was replaced by the round sphere water box? Anything wrong
> I have made?
>

You've simulated a bunch of molecules that diffuse. What shape would you
expect for the envelope of the diffusion? How would it vary over time?

Further, by visual check if in a production MD I did not see residue
> disconnection caused by "Periodic_Boundary_Conditions", can we guarantee no
> minor disconnection occurred during the md (or significant bond length
> variance unobservable by the naked eye with pymol) if we did not process
> the trjconv correction step?
>

The forces produced by such a disconnection would blow everything up
immediately. Since it didn't...

Mark


> I am looking forward to getting a reply from you.
>
>
> Brett
>
>
>
>
>
>
> At 2016-04-14 20:02:43, "Mark Abraham"  wrote:
> >Hi,
> >
> >If this "separation" was real, would you have expected to see
> >
> >a) a massive spike in the potential energy
> >b) complete inability for the constraint algorithm to enforce bond
> lengths?
> >
> >Hint, you haven't seen that.
> >
> >Mark
> >
> >On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/14/16 5:35 AM, Brett wrote:
> >> > Dear All,
> >> >
> >> >
> >> >
> >> > Thanks the reply.
> >> >
> >> >
> >> > But I think I need to discuss with you further on whether I need to
> >> discontinue my production MD. As I mentioned, resi 366-367 separated
> from
> >> the major body of the protein. By pymol I find resi 366-367 were at one
> >> edge of the box and were almost outside of the water box, and its
> >> neighbouring residues resi 365 and resi 368 were at the opposite edge of
> >> the box and were also almost outside of the water box.
> >> >
> >> >
> >> > It seems that way, although at the initial step by editconf I have put
> >> the protein in the center of the cubic box (1.5 nm), during the first 6
> ns
> >> the protein has moved significantly in the box, and at some moment resi
> >> 366-367 have moved out of the box, leading to the disconnection of resi
> >> 366-367 from the major body of the protein and finally leading to resi
> >> 366-367 at the opposite of  its neighbouring residues resi 365 and resi
> 368
> >> in the cubix box.
> >> >
> >> >
> >> > Am I right?
> >> >
> >>
> >> Diffusion is normal.  The residues are not actually disconnected.  You
> can
> >> use
> >> trjconv to "fix" this state, but there is nothing physically wrong with
> it.
> >> mdrun cares about physics, not our visualization convenience.
> >>
> >> -Justin
> >>
> >> >
> >> > Brett
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > At 2016-04-14 16:31:20, "Mark Abraham" 
> wrote:
> >> >> Hi,
> >> >>
> >> >> As the link Justin gave you says, and Tsjerk has since confirmed,
> this
> >> is
> >> >> normal. There are infinitely many equivalent representations of your
> >> >> simulation, not all of which will look connected for the thing that
> is
> >> of
> >> >> interest.
> >> >>
> >> >> Strategies for handling visualisation are also on that link, but you
> >> don't
> >> >> need to handle anything within the simulation.
> >> >>
> >> >> Mark
> >> >>
> >> >> On Thu, 14 Apr 2016 09:48 Brett  wrote:
> >> >>
> >> >>> Dear All,
> >> >>>
> >> >>> As I have introduced in my previous e-mail,
> >> >>>
> >> >>> "After energy minimization and equilibrations, I am now running a
> 50 ns
> >> >>> production MD, for a protein of 6 identical subunits, with each
> subunit
> >> >>> about 300 residues (from resi 120 to resi 420), and there were no
> >> breaks in
> >> >>> any chain. Every day it runs about 1 ns, and every day I use the
> >> command
> >> >>> trjconv to get a new PDB based on the md_0_1.trr file, for the
> >> comparison
> >> >>> between the new pdb and the initial pdb.
> >> >>>
> >> >>>
> >> >>> Today I got the PDB at 6 ns. However when I checked it my pymol, I
> find
> >> >>> there is something very strange. Although the rmsd between the 6 ns
> md
> >> PDB
> >> >>> and 0ns md PDB was about only 3.7, for chain B, residue 366-367
> moved
> >> 180
> >> >>> angstrom away from this residues neighbouring residues, and
> >> correspondingly
> >> >>> make chain B has a break at residue 366-367!"
> >> >>>
> >> >>> A moment ago by trjconv I regot the6 ns pdb with water, I find

[gmx-users] further on: very strange phenomenon for my production MD by gromacs

2016-04-15 Thread Brett

Dear All,

By xmgrace I have checked the xmgrace, I find the spike was between -8.245e+06 
and -8.225e+06, is the spike massive or not?


In addition, by
gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump 
-dump 6000,


I got the 6 ns with water pdb and I have checked the pdb (with water box), I 
find the resi 366-367 were not disconnected!


However, by gmx editconf, the original water box was in cubic, after "gmx 
trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump -dump 
6000", the cubic water box was replaced by a rough sphere water box with the 
protein roughly in the center. Will you please explain why the cubic water box 
was replaced by the round sphere water box? Anything wrong I have made?


Further, by visual check if in a production MD I did not see residue 
disconnection caused by "Periodic_Boundary_Conditions", can we guarantee no 
minor disconnection occurred during the md (or significant bond length variance 
unobservable by the naked eye with pymol) if we did not process the trjconv 
correction step?


I am looking forward to getting a reply from you.


Brett






At 2016-04-14 20:02:43, "Mark Abraham"  wrote:
>Hi,
>
>If this "separation" was real, would you have expected to see
>
>a) a massive spike in the potential energy
>b) complete inability for the constraint algorithm to enforce bond lengths?
>
>Hint, you haven't seen that.
>
>Mark
>
>On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul  wrote:
>
>>
>>
>> On 4/14/16 5:35 AM, Brett wrote:
>> > Dear All,
>> >
>> >
>> >
>> > Thanks the reply.
>> >
>> >
>> > But I think I need to discuss with you further on whether I need to
>> discontinue my production MD. As I mentioned, resi 366-367 separated from
>> the major body of the protein. By pymol I find resi 366-367 were at one
>> edge of the box and were almost outside of the water box, and its
>> neighbouring residues resi 365 and resi 368 were at the opposite edge of
>> the box and were also almost outside of the water box.
>> >
>> >
>> > It seems that way, although at the initial step by editconf I have put
>> the protein in the center of the cubic box (1.5 nm), during the first 6 ns
>> the protein has moved significantly in the box, and at some moment resi
>> 366-367 have moved out of the box, leading to the disconnection of resi
>> 366-367 from the major body of the protein and finally leading to resi
>> 366-367 at the opposite of  its neighbouring residues resi 365 and resi 368
>> in the cubix box.
>> >
>> >
>> > Am I right?
>> >
>>
>> Diffusion is normal.  The residues are not actually disconnected.  You can
>> use
>> trjconv to "fix" this state, but there is nothing physically wrong with it.
>> mdrun cares about physics, not our visualization convenience.
>>
>> -Justin
>>
>> >
>> > Brett
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > At 2016-04-14 16:31:20, "Mark Abraham"  wrote:
>> >> Hi,
>> >>
>> >> As the link Justin gave you says, and Tsjerk has since confirmed, this
>> is
>> >> normal. There are infinitely many equivalent representations of your
>> >> simulation, not all of which will look connected for the thing that is
>> of
>> >> interest.
>> >>
>> >> Strategies for handling visualisation are also on that link, but you
>> don't
>> >> need to handle anything within the simulation.
>> >>
>> >> Mark
>> >>
>> >> On Thu, 14 Apr 2016 09:48 Brett  wrote:
>> >>
>> >>> Dear All,
>> >>>
>> >>> As I have introduced in my previous e-mail,
>> >>>
>> >>> "After energy minimization and equilibrations, I am now running a 50 ns
>> >>> production MD, for a protein of 6 identical subunits, with each subunit
>> >>> about 300 residues (from resi 120 to resi 420), and there were no
>> breaks in
>> >>> any chain. Every day it runs about 1 ns, and every day I use the
>> command
>> >>> trjconv to get a new PDB based on the md_0_1.trr file, for the
>> comparison
>> >>> between the new pdb and the initial pdb.
>> >>>
>> >>>
>> >>> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
>> >>> there is something very strange. Although the rmsd between the 6 ns md
>> PDB
>> >>> and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved
>> 180
>> >>> angstrom away from this residues neighbouring residues, and
>> correspondingly
>> >>> make chain B has a break at residue 366-367!"
>> >>>
>> >>> A moment ago by trjconv I regot the6 ns pdb with water, I find the
>> residue
>> >>> 366-367 are almost (or exactly) at the edge of the water box (but by
>> naked
>> >>> eye it seems the residue 366-367 are not outside of the water box). In
>> this
>> >>> does the moving away of the residue 366-367 are still caused by "
>> >>> Periodic_Boundary_Conditions", and can I continue the production md to
>> >>> completion with the residue 366-367 disconnected from the major part
>> of the
>> >>> protein complex and then I correct it by trjconv?
>> >>>
>> >>> I am looking forward to getting a reply from you.
>> >>>
>> >>>
>> >>> Brett
>> >>>
>> >>>
>> >>

[gmx-users] (no subject)

2016-04-15 Thread ali osouli

Dear all
My MD run movie shows that my ligand jump out of protein in the early
picoseconds of simulation, does anybody knwos which step of my MD should i
check?
In additon to rutin steps i have included a distance restraint file to
topolgy.itp.
Best regards Ali
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Re: [gmx-users] Osmotic pressure

2016-04-15 Thread gozde ergin

Hi Mark,

I use Berendsen for T and P-coupl.
Do you think I should change them?

> On 15 Apr 2016, at 11:55, Mark Abraham  wrote:
> 
> Hi,
> 
> Also you can choose coupling algorithms that are known to sample correct
> ensembles...
> 
> Mark
> 
> On Fri, 15 Apr 2016 11:50 Justin Lemkul  wrote:
> 
>> 
>> 
>> On 4/15/16 5:20 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I simulate the NaCl solution to estimate the osmotic pressure. My salt
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
>> molecules.
>>> I use CHARMM36 ff with NBFIX correction.
>>> 
>>> After the simulation I extract the z-coordinates of restraint ions and
>> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
>> pressure.
>>> Actually I try to get the similar results as Lou&Roux 2010 study.
>>> 
>>> However my osmotic pressure results are on the line of ideal solution
>> osmotic pressure as shown equation in below;
>>> 
>>> P = cRT (Van’t Hoff equation)
>>> 
>>> but not the similar result with experiments.
>>> 
>> 
>> What values do you actually get?  How do they compare with the values from
>> the
>> Roux paper?  Are you remembering to divide by 2*area in your calculation
>> (since
>> you have two walls)?
>> 
>>> Is there anyone here that get the same trend as me for osmotic pressure
>> calculation? Or is there something that I miss?
>>> 
>>> 
>>> Here is my .mdp file;
>>> 
>>> define   = -DPOSRES
>>> integrator   = md
>>> dt   = 0.002
>>> nsteps   = 250   ;
>>> ; Output control
>>> nstxout  = 2000
>>> nstvout  = 2000
>>> nstlog   = 2000
>>> nstenergy= 2000
>>> ; Bond parameters
>>> continuation = no;
>>> constraint_algorithm = shake ; h
>>> constraints  = all-bonds ; a
>>> shake_tol= 0.0001
>>> ; Neighborsearching
>>> ns_type = grid  ;
>>> nstlist = 5 ;
>>> rlist   = 1.1   ;
>>> rcoulomb= 1.1   ;
>>> rvdw= 1.1   ;
>> 
>> These nonbonded settings are wrong.  The values for CHARMM36 are well
>> established and you should not deviate from them.
>> 
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>> 
>> -Justin
>> 
>>> ; Electrostatics
>>> coulombtype = PME   ;
>>> pme_order   = 4 ;
>>> fourierspacing  = 0.16  ;
>>> 
>>> tcoupl   = berendsen
>>> tc-grps  = System
>>> tau_t= 1.0
>>> ref_t= 300
>>> ; Pressure coupling is on
>>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
>> weak coupling
>>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
>> vectors
>>> tau_p   = 2.0 2.0  ; time constant, in ps
>>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>>> compressibility = 0 4.5e-5; isothermal compressibility,
>> bar^-1
>>> refcoord_scaling= com
>>> ; Periodic boundary conditions
>>> pbc = xyz   ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes   ; Velocity generation is on
>>> gen_temp= 300   ; temperature for velocity generation
>>> gen_seed= -1; random seed
>>> ; COM motion removal
>>> ; These options remove COM motion of the system
>>> nstcomm = 10
>>> comm-mode   = Linear
>>> comm-grps   = System
>>> 
>>> 
>> 
>> --
>> ==
>> 
>> 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
>> 
>> ==
>> --
>> 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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Re: [gmx-users] Osmotic pressure

2016-04-15 Thread gozde ergin

Justin thank you very much for your quick respond. These values that I get, for 
ideal solution and in Roux paper are shown below ;

Osmotic pressure for 3M : My result 156 bar
  Ideal solution 150 bar
  Roux study ~155 bar

Osmotic pressure for 4M : My result 194 bar
  Ideal solution 200 bar
  Roux study ~220 bar

Osmotic pressure for 5M : My result 251 bar
  Ideal solution 250 bar
  Roux study ~300 bar

Yes I divide in two for two walls. Ok I rerun the simulation with these new 
settings.

Thanks a lot.
> On 15 Apr 2016, at 11:50, Justin Lemkul  wrote:
> 
> 
> 
> On 4/15/16 5:20 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I simulate the NaCl solution to estimate the osmotic pressure. My salt 
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the 
>> molecules.
>> I use CHARMM36 ff with NBFIX correction.
>> 
>> After the simulation I extract the z-coordinates of restraint ions and use 
>> the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic 
>> pressure.
>> Actually I try to get the similar results as Lou&Roux 2010 study.
>> 
>> However my osmotic pressure results are on the line of ideal solution 
>> osmotic pressure as shown equation in below;
>> 
>> P = cRT (Van’t Hoff equation)
>> 
>> but not the similar result with experiments.
>> 
> 
> What values do you actually get?  How do they compare with the values from 
> the Roux paper?  Are you remembering to divide by 2*area in your calculation 
> (since you have two walls)?
> 
>> Is there anyone here that get the same trend as me for osmotic pressure 
>> calculation? Or is there something that I miss?
>> 
>> 
>> Here is my .mdp file;
>> 
>> define   = -DPOSRES
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 250   ;
>> ; Output control
>> nstxout  = 2000
>> nstvout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> ; Bond parameters
>> continuation = no;
>> constraint_algorithm = shake ; h
>> constraints  = all-bonds ; a
>> shake_tol= 0.0001
>> ; Neighborsearching
>> ns_type = grid  ;
>> nstlist = 5 ;
>> rlist   = 1.1   ;
>> rcoulomb= 1.1   ;
>> rvdw= 1.1   ;
> 
> These nonbonded settings are wrong.  The values for CHARMM36 are well 
> established and you should not deviate from them.
> 
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM 
> 
> 
> -Justin
> 
>> ; Electrostatics
>> coulombtype = PME   ;
>> pme_order   = 4 ;
>> fourierspacing  = 0.16  ;
>> 
>> tcoupl   = berendsen
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> ; Pressure coupling is on
>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
>> coupling
>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box 
>> vectors
>> tau_p   = 2.0 2.0  ; time constant, in ps
>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>> compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
>> refcoord_scaling= com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; Velocity generation is on
>> gen_temp= 300   ; temperature for velocity generation
>> gen_seed= -1; random seed
>> ; COM motion removal
>> ; These options remove COM motion of the system
>> nstcomm = 10
>> comm-mode   = Linear
>> comm-grps   = System
>> 
>> 
> 
> -- 
> ==
> 
> 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 
> 
> 
> ==
> -- 
> 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 
> <

Re: [gmx-users] Osmotic pressure

2016-04-15 Thread Mark Abraham

Hi,

Also you can choose coupling algorithms that are known to sample correct
ensembles...

Mark

On Fri, 15 Apr 2016 11:50 Justin Lemkul  wrote:

>
>
> On 4/15/16 5:20 AM, gozde ergin wrote:
> > Dear all,
> >
> > I simulate the NaCl solution to estimate the osmotic pressure. My salt
> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> molecules.
> > I use CHARMM36 ff with NBFIX correction.
> >
> > After the simulation I extract the z-coordinates of restraint ions and
> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
> pressure.
> > Actually I try to get the similar results as Lou&Roux 2010 study.
> >
> > However my osmotic pressure results are on the line of ideal solution
> osmotic pressure as shown equation in below;
> >
> > P = cRT (Van’t Hoff equation)
> >
> > but not the similar result with experiments.
> >
>
> What values do you actually get?  How do they compare with the values from
> the
> Roux paper?  Are you remembering to divide by 2*area in your calculation
> (since
> you have two walls)?
>
> > Is there anyone here that get the same trend as me for osmotic pressure
> calculation? Or is there something that I miss?
> >
> >
> > Here is my .mdp file;
> >
> > define   = -DPOSRES
> > integrator   = md
> > dt   = 0.002
> > nsteps   = 250   ;
> > ; Output control
> > nstxout  = 2000
> > nstvout  = 2000
> > nstlog   = 2000
> > nstenergy= 2000
> > ; Bond parameters
> > continuation = no;
> > constraint_algorithm = shake ; h
> > constraints  = all-bonds ; a
> > shake_tol= 0.0001
> > ; Neighborsearching
> > ns_type = grid  ;
> > nstlist = 5 ;
> > rlist   = 1.1   ;
> > rcoulomb= 1.1   ;
> > rvdw= 1.1   ;
>
> These nonbonded settings are wrong.  The values for CHARMM36 are well
> established and you should not deviate from them.
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> -Justin
>
> > ; Electrostatics
> > coulombtype = PME   ;
> > pme_order   = 4 ;
> > fourierspacing  = 0.16  ;
> >
> > tcoupl   = berendsen
> > tc-grps  = System
> > tau_t= 1.0
> > ref_t= 300
> > ; Pressure coupling is on
> > pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> weak coupling
> > pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
> vectors
> > tau_p   = 2.0 2.0  ; time constant, in ps
> > ref_p   = 1.0 1.0  ; reference pressure (in bar)
> > compressibility = 0 4.5e-5; isothermal compressibility,
> bar^-1
> > refcoord_scaling= com
> > ; Periodic boundary conditions
> > pbc = xyz   ; 3-D PBC
> > ; Dispersion correction
> > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes   ; Velocity generation is on
> > gen_temp= 300   ; temperature for velocity generation
> > gen_seed= -1; random seed
> > ; COM motion removal
> > ; These options remove COM motion of the system
> > nstcomm = 10
> > comm-mode   = Linear
> > comm-grps   = System
> >
> >
>
> --
> ==
>
> 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
>
> ==
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Osmotic pressure

2016-04-15 Thread Justin Lemkul




On 4/15/16 5:20 AM, gozde ergin wrote:

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt 
concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules.
I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and use the 
equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure.
Actually I try to get the similar results as Lou&Roux 2010 study.

However my osmotic pressure results are on the line of ideal solution osmotic 
pressure as shown equation in below;

P = cRT (Van’t Hoff equation)

but not the similar result with experiments.



What values do you actually get?  How do they compare with the values from the 
Roux paper?  Are you remembering to divide by 2*area in your calculation (since 
you have two walls)?



Is there anyone here that get the same trend as me for osmotic pressure 
calculation? Or is there something that I miss?


Here is my .mdp file;

define   = -DPOSRES
integrator   = md
dt   = 0.002
nsteps   = 250   ;
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no;
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ;
nstlist = 5 ;
rlist   = 1.1   ;
rcoulomb= 1.1   ;
rvdw= 1.1   ;


These nonbonded settings are wrong.  The values for CHARMM36 are well 
established and you should not deviate from them.


http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

-Justin


; Electrostatics
coulombtype = PME   ;
pme_order   = 4 ;
fourierspacing  = 0.16  ;

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = semiisotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System




--
==

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] pdb2gmx disulfide bond in dimer

2016-04-15 Thread Justin Lemkul




On 4/14/16 9:53 AM, s.varriale wrote:

thank you Justin, but I can't understand how to solve my  problem.
when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique chain
because  N- and C- termini of 2 chains are linked.



As it should.  The two chains have to be merged into a single [moleculetype] 
definition for that bond to be created.  The merging process isn't causing 
stability; some other aspect of your structure is.  The link I provided includes 
all the usual diagnostic information.  Unless you go through those steps (and 
have a look through some of the other million or so posts regarding the same 
issue) and provide some more useful details about what you observe, there's 
little anyone else can suggest.


-Justin


Sonia
Il 14/04/2016 13:46 Justin Lemkul ha scritto:

On 4/14/16 6:32 AM, s.varriale wrote:


Dear all,
I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4.
I do:
pdb2gmx -f prot.pdb -chainsep ter
and the programme generates a .gro file with disulfide bond.
but when i want to minimize the system, there is an error:

There were 2 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is larger
than the 1-4 table size 2.200 nm

if I try to simulate the 2 chains separatly, there is any error.
What can i do?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-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

==




--
==

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] what is the source of "CHL1" cholesterol in the gromacs charmm port?

2016-04-15 Thread Justin Lemkul




On 4/15/16 1:29 AM, Christopher Neale wrote:


Dear Users:

When I look at charmm36-jun2015.ff/merged.rtp downloaded from
http://mackerell.umaryland.edu/charmm_ff.shtml , it has a cholesterol
molecule named CHL1. However, I do not find such a molecule in the
charmm-specific toppar_c36_feb16.tgz downloaded from the same site. In the


Just a note to everyone: as the dates should make very obvious, the Feb 2016 
release of the CHARMM force field is much newer than the port; you should not 
expect exact agreement between these files.  I have not yet made an updated 
port, but it's on my to-do list.



later tarball, I do find cholestrol as "RESI CLOL" in top_all36_cgenff.rtf
but that is from cgenff and the values differ. As a simple proof of the
difference, the charge on O3 is not the same, though the differences extend
beyond that.

Some comments in the charmm-format files refer to
toppar_all27_lipid_cholesterol.str , but I can not find that file ... I
checked in toppar_c31b1.tar.gz from the same website but to no avail.

So my question is what is the source for CHL1 in
charmm36-jun2015.ff/merged.rtp ?



toppar/stream/lipid/toppar_all36_lipid_cholesterol.str

Many residues come from the stream files (either from residues found there or 
created from patches therein).


-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] How to calculate the interaction energy between twomolecules

2016-04-15 Thread Mark Abraham

Hi,

Also you need suitable energy groups. Best done in a rerun after the
simulation.

Mark

On Fri, 15 Apr 2016 10:51 Riccardo Concu  wrote:

> Dear,
> you should use the g_energy tool. Remember to include the .ndx file in your
> command line.
> Regards,
> Riccardo
>
> -Original Message-
> From: 李睿
> Sent: Friday, April 15, 2016 10:23 AM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] How to calculate the interaction energy between
> twomolecules
>
>
> Hello everyone,
> I have a question to ask you to help
> I have two molecules A and B in my simulation system, and they are very
> close.
> I want to know how to calculate their interaction energy after energy
> minimization in gromacs
> Thank you
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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> send a
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[gmx-users] Osmotic pressure

2016-04-15 Thread gozde ergin

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt 
concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules.
I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and use the 
equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure.
Actually I try to get the similar results as Lou&Roux 2010 study.

However my osmotic pressure results are on the line of ideal solution osmotic 
pressure as shown equation in below; 

P = cRT (Van’t Hoff equation) 

but not the similar result with experiments. 

Is there anyone here that get the same trend as me for osmotic pressure 
calculation? Or is there something that I miss?


Here is my .mdp file;

define   = -DPOSRES
integrator   = md 
dt   = 0.002
nsteps   = 250   ; 
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no; 
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ; 
nstlist = 5 ; 
rlist   = 1.1   ; 
rcoulomb= 1.1   ; 
rvdw= 1.1   ; 
; Electrostatics
coulombtype = PME   ; 
pme_order   = 4 ; 
fourierspacing  = 0.16  ; 

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = semiisotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System 


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Re: [gmx-users] How to calculate the interaction energy between twomolecules

2016-04-15 Thread Riccardo Concu


Dear,
you should use the g_energy tool. Remember to include the .ndx file in your 
command line.

Regards,
Riccardo

-Original Message- 
From: 李睿

Sent: Friday, April 15, 2016 10:23 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] How to calculate the interaction energy between 
twomolecules



Hello everyone,
I have a question to ask you to help
I have two molecules A and B in my simulation system, and they are very 
close.
I want to know how to calculate their interaction energy after energy 
minimization in gromacs

Thank you
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[gmx-users] How to calculate the interaction energy between two molecules

2016-04-15 Thread 李睿


Hello everyone,
I have a question to ask you to help
I have two molecules A and B in my simulation system, and they are very close.
I want to know how to calculate their interaction energy after energy 
minimization in gromacs
Thank you
-- 
Gromacs Users mailing list

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Re: [gmx-users] what is the source of "CHL1" cholesterol in the gromacs charmm port?

Re: [gmx-users] Effect of bond constraints on equilibrium densities of equilibrated liquids

[gmx-users] Effect of bond constraints on equilibrium densities of equilibrated liquids

Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs

Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs

[gmx-users] MARTINI simulation of protein-protein recognition

Re: [gmx-users] (no subject)

Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs

[gmx-users] further on: very strange phenomenon for my production MD by gromacs

[gmx-users] (no subject)

Re: [gmx-users] Osmotic pressure

Re: [gmx-users] Osmotic pressure

Re: [gmx-users] Osmotic pressure

Re: [gmx-users] Osmotic pressure

Re: [gmx-users] pdb2gmx disulfide bond in dimer

Re: [gmx-users] what is the source of "CHL1" cholesterol in the gromacs charmm port?

Re: [gmx-users] How to calculate the interaction energy between twomolecules

[gmx-users] Osmotic pressure

Re: [gmx-users] How to calculate the interaction energy between twomolecules

[gmx-users] How to calculate the interaction energy between two molecules

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