Re: [gmx-users] to neutralize the system

[Tsjerk Wassenaar]

Hi Qasim,

Not only should you neutralize the system, but you should add additional
ions too. The behaviour of charged side chains which can find a partner ion
from solution is different from those that can't. You won't see any
problems, but the results will be affected. Not coming across any problems
is not good quality assurance in simulations.

Cheers,

Tsjerk
On Jun 15, 2016 00:01, "Qasim Pars"  wrote:

Dear gmx users,

I am confused on below questions:

1) Is it necessary to neutralize a protein without ligand?  Does the PME
method work with a charged protein correctly?

2) I have done lots of MD simulations at a charged complex structure
(protein+ligand) with the PME method using GROMACS. I haven't come across
with any problems because of the charge of the system. It means that the
PME method works at a charged complex system properly. In spite of that, do
you think that I need to neutralize a charged complex system?

Can anyone comment on above questions?

Cheers,

--
Qasim Pars
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[gmx-users] How to add solvent in a Biphasic Systems ?

[Jinfeng Huang]

Dear gromacs users,


I want to build a liquid-solid system following the tutorial "Building 
Biphasic Systems" 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
 ), but I have met two problems during my operation.


1) After adding a protein to the liquid layer, the tutorial describe as 
"Then proceed with another round of solvate to add water, as before." I don't 
know how to add the water. I used the "solvate" command and there will be a lot 
of waters added in the solid layer (There are no waters added in the solid 
layer after I changed the value of the C radius when I solvate the solid layer 
only). How should I solvate the protein-solid system without waters added in 
the solid layer?


2)How to add TIP3P water models with the solvate command in gromacs instead 
of the spc216 water model?
   It's highly appreciated if there are any suggestions.
Jingfeng




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[gmx-users] to neutralize the system

[Qasim Pars]

Dear gmx users,

I am confused on below questions:

1) Is it necessary to neutralize a protein without ligand?  Does the PME
method work with a charged protein correctly?

2) I have done lots of MD simulations at a charged complex structure
(protein+ligand) with the PME method using GROMACS. I haven't come across
with any problems because of the charge of the system. It means that the
PME method works at a charged complex system properly. In spite of that, do
you think that I need to neutralize a charged complex system?

Can anyone comment on above questions?

Cheers,

-- 
Qasim Pars
-- 
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Re: [gmx-users] Lipid parameterization

[Mohsen Ramezanpour]

Thanks Justin, Chris,

I will give it a try and follow what you suggested.

Cheers
Mohsen

On Tue, Jun 14, 2016 at 2:35 PM, Justin Lemkul  wrote:

>
>
> On 6/14/16 2:04 PM, Christopher Neale wrote:
>
>> You might see if CHARMM_GUI has parameters for it. This is not to say that
>> they will be amazing parameters, as I have not looked into their approach
>> to
>> generate parameters and it may well be rational cut and paste, but they do
>> have parameters for loads of lipids. If they don't have parameters, you
>> might
>> also consider asking them to put your HG on their to-do list. My
>> understanding is that they want to add useful moieties.
>>
>>
> CHARMM-GUI has access to the full CHARMM force field, and the full
> complement of every lipid parametrized for it (which is indeed quite
> extensive).  If a particular molecule (lipid type) is missing, it will call
> ParamChem (the CGenFF program's web server) to generate a topology for the
> full molecule.  As I said in my first reply, this would be suboptimal as
> most of the necessary parameters will already be in the highly optimized
> CHARMM36 lipid force field.  Without knowing what the OP wants to work
> with, it's hard to say further, but I expect most of the work will already
> be done, and one needs to address a suitable model compound or two to work
> out any new linkages.
>
> -Justin
>
>
> Chris.
>>
>>  From:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>>  on behalf of Mohsen
>> Ramezanpour  Sent: 14 June 2016 13:53:26
>> To:
>> Discussion list for GROMACS users Subject: [gmx-users] Lipid
>> parameterization
>>
>> Dear Gromacs users,
>>
>> I am trying to parameterize a lipid molecule with a weird headgroup :-) in
>> Charmm36 force field for doing simulation in GROMACS. Reading through
>> literature, I found that Swissparam, and Paramchem.org are two useful
>> tools
>> to make the topology files automatically.
>>
>> However, both seems to be suitable for small drug-like molecules than
>> large
>> biological molecules, like lipids. Swissparam is a mixture of charmm
>> parameters and MMFF and is not based on any specific CHARMM FF version.
>> Paramcharm has also recommended to not use it for biological molecules.
>>
>> Although lipids are biological molecules, but I was wondering what will
>> happen if we consider the "whole synthetic lipid" as a drug-like molecule.
>>
>>
>> In this case, we might be able to mix it with other lipids which have been
>> parameterized in Charmm36?
>>
>> Thanks in advance for your comments Cheers Mohsen -- *Rewards work better
>> than punishment ...* -- 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
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a
>> mail to gmx-users-requ...@gromacs.org.
>>
>>
> --
> ==
>
> 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
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
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Re: [gmx-users] Lipid parameterization

[Justin Lemkul]

On 6/14/16 2:04 PM, Christopher Neale wrote:

You might see if CHARMM_GUI has parameters for it. This is not to say that
they will be amazing parameters, as I have not looked into their approach to
generate parameters and it may well be rational cut and paste, but they do
have parameters for loads of lipids. If they don't have parameters, you might
also consider asking them to put your HG on their to-do list. My
understanding is that they want to add useful moieties.



CHARMM-GUI has access to the full CHARMM force field, and the full complement of 
every lipid parametrized for it (which is indeed quite extensive).  If a 
particular molecule (lipid type) is missing, it will call ParamChem (the CGenFF 
program's web server) to generate a topology for the full molecule.  As I said 
in my first reply, this would be suboptimal as most of the necessary parameters 
will already be in the highly optimized CHARMM36 lipid force field.  Without 
knowing what the OP wants to work with, it's hard to say further, but I expect 
most of the work will already be done, and one needs to address a suitable model 
compound or two to work out any new linkages.


-Justin


Chris.

 From:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 on behalf of Mohsen
Ramezanpour  Sent: 14 June 2016 13:53:26 To:
Discussion list for GROMACS users Subject: [gmx-users] Lipid
parameterization

Dear Gromacs users,

I am trying to parameterize a lipid molecule with a weird headgroup :-) in
Charmm36 force field for doing simulation in GROMACS. Reading through
literature, I found that Swissparam, and Paramchem.org are two useful tools
to make the topology files automatically.

However, both seems to be suitable for small drug-like molecules than large
biological molecules, like lipids. Swissparam is a mixture of charmm
parameters and MMFF and is not based on any specific CHARMM FF version.
Paramcharm has also recommended to not use it for biological molecules.

Although lipids are biological molecules, but I was wondering what will
happen if we consider the "whole synthetic lipid" as a drug-like molecule.


In this case, we might be able to mix it with other lipids which have been
parameterized in Charmm36?

Thanks in advance for your comments Cheers Mohsen -- *Rewards work better
than punishment ...* -- 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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.



--
==

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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Gromacs Users mailing list

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Re: [gmx-users] Decreased Area/Lipid of Lipid Bilayer for CHARMM-GUI

[Justin Lemkul]

On 6/14/16 2:10 PM, Nidhin Thomas wrote:

Hi Dr. Neale/ Dr. Lemkul,

I have simulated DPPC bilayer for 12 nanoseconds now. The average APL is 0.608 
nm^2 now with a standard deviation of 0.016.
he initial dip in the APL (from 0.63 to 0.599) was found at the beginning of 
NPT itself.

Therefore I think, I should just run more time and it should give a good result 
around 0.61 nm^2.

Dr. Lemkul had given me the links of few research papers and in one of the 
paper, the surface area per lipid for DPPC bilayer was found out to be 0.604 
+/- 0.1 nm^2 for force based switching functions for LJ interactions with 10-12 
Angstrom cut-off .

I do not know if 0.61 nm^ APL (from 0.63 nm^2) is an acceptable result for DPPC 
and I can continue analyze the results further.



12 ns is at least an order of magnitude shorter than what is normally necessary 
for membranes.  The result is not surprising and in good agreement with 
expectations.  But that doesn't mean the simulation is long enough; you just 
happen to have one quantity that works out well at this point.


-Justin


Thanks a lot for helping me out,

Nidhin Thomas
University of Houston

--

Message: 3
Date: Tue, 14 Jun 2016 16:51:33 +
From: Christopher Neale 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from
CHARMM-GUI
Message-ID:



Content-Type: text/plain; charset="us-ascii"

How long are your simulations? I build a DPPC bilayer with charmm-GUI and 
simulate for 300 ns at 323 K and the APL has a mean of 0.61 nm^2 and a standard 
deviation of 0.01 nm^2. However, the APL does happen to dip down to 0.59 within 
10 ns... it's just that the fluctuations will also sometimes take it as high as 
0.65 and as low as 0.57. Maybe give us your simulation time and upload a plot 
of APL vs. time and post the link here (no direct attachments please). If 
you're running 10-20 ns and you see the APL get low then you may simply need to 
run for longer.

Here is the data from my simulation of DPPC at 323K:
https://www.dropbox.com/s/adu4ft8dhuyc9c2/dppc_323k_apl.pdf?dl=0

I suggest you figure things out with DPPC before moving on to your PA lipids.

Chris.


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

Sent: 13 June 2016 19:32:47
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

Hello everyone,

I have also given below the map file that I have used for equilibration.

integrator = md
dt = 0.002
nsteps = 200
nstlog = 1000
nstxout = 5000
nstvout = 1000
nstfout = 1000
nstcalcenergy = 100
nstxtcout   = 1000
nstenergy = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps = MEMB SOL_ION
tau_t = 1.0 1.0
ref_t = 323.15 323.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = MEMB SOL_ION
;
refcoord_scaling = com


Thanks,

Nidhin Thomas
University of Houston


Message: 4
Date: Mon, 13 Jun 2016 17:51:43 +
From: Christopher Neale 
To: "gromacs.org_gmx-users@maillist.sys.kth.se"
 , "gmx-us...@gromacs.org"
 
Subject: Re: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer
 obtainedfrom CHARMM-GUI
Message-ID:
 


Content-Type: text/plain; charset="Windows-1252"

In future posts, it is best to copy and paste your .mdp file because we can not 
all get attachments from the list.

Regarding your results, it is my understanding that the CHARMM-GUI has 
parameters for, and can build, many lipids systems whose parameters have not 
been completely validated by simulations in the literature (e.g. for things 
like APL). Last time I looked, PG was the only anionic charmm36 lipid that was 
shown to behave properly in bilayers (Klauda), though others may have since 
been shown to work well.

If the issue is not simply that the PA parameters are not very good, then one 
likely source of problem is that perhaps you are not using the NBfix ions? That 
could be a big deal. I never use Na with membranes for this reason, so you 
could try KCl instead.

Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on 

[gmx-users] Decreased Area/Lipid of Lipid Bilayer for CHARMM-GUI

[Nidhin Thomas]

Hi Dr. Neale/ Dr. Lemkul,

I have simulated DPPC bilayer for 12 nanoseconds now. The average APL is 0.608 
nm^2 now with a standard deviation of 0.016.
he initial dip in the APL (from 0.63 to 0.599) was found at the beginning of 
NPT itself.

Therefore I think, I should just run more time and it should give a good result 
around 0.61 nm^2.

Dr. Lemkul had given me the links of few research papers and in one of the 
paper, the surface area per lipid for DPPC bilayer was found out to be 0.604 
+/- 0.1 nm^2 for force based switching functions for LJ interactions with 10-12 
Angstrom cut-off .

I do not know if 0.61 nm^ APL (from 0.63 nm^2) is an acceptable result for DPPC 
and I can continue analyze the results further.

Thanks a lot for helping me out,

Nidhin Thomas
University of Houston
> --
> 
> Message: 3
> Date: Tue, 14 Jun 2016 16:51:33 +
> From: Christopher Neale 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from
>   CHARMM-GUI
> Message-ID:
>   
> 
>   
> Content-Type: text/plain; charset="us-ascii"
> 
> How long are your simulations? I build a DPPC bilayer with charmm-GUI and 
> simulate for 300 ns at 323 K and the APL has a mean of 0.61 nm^2 and a 
> standard deviation of 0.01 nm^2. However, the APL does happen to dip down to 
> 0.59 within 10 ns... it's just that the fluctuations will also sometimes take 
> it as high as 0.65 and as low as 0.57. Maybe give us your simulation time and 
> upload a plot of APL vs. time and post the link here (no direct attachments 
> please). If you're running 10-20 ns and you see the APL get low then you may 
> simply need to run for longer.
> 
> Here is the data from my simulation of DPPC at 323K:
> https://www.dropbox.com/s/adu4ft8dhuyc9c2/dppc_323k_apl.pdf?dl=0
> 
> I suggest you figure things out with DPPC before moving on to your PA lipids.
> 
> Chris.
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Nidhin 
> Thomas 
> Sent: 13 June 2016 19:32:47
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI
> 
> Hello everyone,
> 
> I have also given below the map file that I have used for equilibration.
> 
> integrator = md
> dt = 0.002
> nsteps = 200
> nstlog = 1000
> nstxout = 5000
> nstvout = 1000
> nstfout = 1000
> nstcalcenergy = 100
> nstxtcout   = 1000
> nstenergy = 1000
> ;
> cutoff-scheme = Verlet
> nstlist = 20
> rlist = 1.2
> coulombtype = pme
> rcoulomb = 1.2
> vdwtype = Cut-off
> vdw-modifier = Force-switch
> rvdw_switch = 1.0
> rvdw = 1.2
> ;
> tcoupl = Nose-Hoover
> tc_grps = MEMB SOL_ION
> tau_t = 1.0 1.0
> ref_t = 323.15 323.15
> ;
> pcoupl = Parrinello-Rahman
> pcoupltype = semiisotropic
> tau_p = 5.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> ;
> constraints = h-bonds
> constraint_algorithm = LINCS
> continuation = yes
> ;
> nstcomm = 100
> comm_mode = linear
> comm_grps = MEMB SOL_ION
> ;
> refcoord_scaling = com
> 
> 
> Thanks,
> 
> Nidhin Thomas
> University of Houston
> 
>> Message: 4
>> Date: Mon, 13 Jun 2016 17:51:43 +
>> From: Christopher Neale 
>> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>>  , "gmx-us...@gromacs.org"
>>  
>> Subject: Re: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer
>>  obtainedfrom CHARMM-GUI
>> Message-ID:
>>  
>> 
>> 
>> Content-Type: text/plain; charset="Windows-1252"
>> 
>> In future posts, it is best to copy and paste your .mdp file because we can 
>> not all get attachments from the list.
>> 
>> Regarding your results, it is my understanding that the CHARMM-GUI has 
>> parameters for, and can build, many lipids systems whose parameters have not 
>> been completely validated by simulations in the literature (e.g. for things 
>> like APL). Last time I looked, PG was the only anionic charmm36 lipid that 
>> was shown to behave properly in bilayers (Klauda), though others may have 
>> since been shown to work well.
>> 
>> If the issue is not simply that the PA parameters are not very good, then 
>> one likely source of problem is that perhaps you are not using the NBfix 
>> ions? That could be a big deal. I never use Na with membranes for this 
>> reason, so you could try KCl instead.
>> 
>> Chris.
>> 
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of Nidhin 
>> Thomas 
>> Sent: 12 June 2016 

Re: [gmx-users] Lipid parameterization

[Christopher Neale]

You might see if CHARMM_GUI has parameters for it. This is not to say that they 
will be amazing parameters, as I have not looked into their approach to 
generate parameters and it may well be rational cut and paste, but they do have 
parameters for loads of lipids. If they don't have parameters, you might also 
consider asking them to put your HG on their to-do list. My understanding is 
that they want to add useful moieties.

Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mohsen 
Ramezanpour 
Sent: 14 June 2016 13:53:26
To: Discussion list for GROMACS users
Subject: [gmx-users] Lipid parameterization

Dear Gromacs users,

I am trying to parameterize a lipid molecule with a weird headgroup :-) in
Charmm36 force field for doing simulation in GROMACS.
Reading through literature, I found that Swissparam, and Paramchem.org are
two useful tools to make the topology files automatically.

However, both seems to be suitable for small drug-like molecules than large
biological molecules, like lipids. Swissparam is a mixture of charmm
parameters and MMFF and is not based on any specific CHARMM FF version.
Paramcharm has also recommended to not use it for biological molecules.

Although lipids are biological molecules, but I was wondering what will
happen if we consider the "whole synthetic lipid" as a drug-like molecule.


In this case, we might be able to mix it with other lipids which have been
parameterized in Charmm36?

Thanks in advance for your comments
Cheers
Mohsen
--
*Rewards work better than punishment ...*
--
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] Lipid parameterization

[Justin Lemkul]

On 6/14/16 1:53 PM, Mohsen Ramezanpour wrote:

Dear Gromacs users,

I am trying to parameterize a lipid molecule with a weird headgroup :-) in
Charmm36 force field for doing simulation in GROMACS.
Reading through literature, I found that Swissparam, and Paramchem.org are
two useful tools to make the topology files automatically.

However, both seems to be suitable for small drug-like molecules than large
biological molecules, like lipids. Swissparam is a mixture of charmm
parameters and MMFF and is not based on any specific CHARMM FF version.
Paramcharm has also recommended to not use it for biological molecules.

Although lipids are biological molecules, but I was wondering what will
happen if we consider the "whole synthetic lipid" as a drug-like molecule.


In this case, we might be able to mix it with other lipids which have been
parameterized in Charmm36?



You should start by using any relevant parameters from the CHARMM36 lipid force 
field, then parametrizing new moieties to be consistent with the lipid force 
field using suitable model compounds.  CGenFF might give OK estimates of initial 
charges, dihedrals, etc. but they should absolutely not be directly combined or 
considered final.  They'll point you in the right direction, but hybridizing 
CGenFF and highly optimized protein/nucleic acid/lipid force fields within the 
same molecule is not a proper approach.


-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

==
--
Gromacs Users mailing list

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[gmx-users] Lipid parameterization

[Mohsen Ramezanpour]

Dear Gromacs users,

I am trying to parameterize a lipid molecule with a weird headgroup :-) in
Charmm36 force field for doing simulation in GROMACS.
Reading through literature, I found that Swissparam, and Paramchem.org are
two useful tools to make the topology files automatically.

However, both seems to be suitable for small drug-like molecules than large
biological molecules, like lipids. Swissparam is a mixture of charmm
parameters and MMFF and is not based on any specific CHARMM FF version.
Paramcharm has also recommended to not use it for biological molecules.

Although lipids are biological molecules, but I was wondering what will
happen if we consider the "whole synthetic lipid" as a drug-like molecule.


In this case, we might be able to mix it with other lipids which have been
parameterized in Charmm36?

Thanks in advance for your comments
Cheers
Mohsen
-- 
*Rewards work better than punishment ...*
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Re: [gmx-users] Gromacs multisubunit defragmentation

[Justin Lemkul]

On 6/14/16 1:13 PM, Muhammad Hagras wrote:

It actually worked now with the option pbc=no (I was previously just
commenting out pbc but it seems it is not the same as pbc=no!),

But with pbc=xyz, it does fragment! Weird! When playing with the box size,
I see different fragmentation patterns!



This implies that the box is not set up correctly.  Using -d 1.0 should have 
taken care of this.  If you're still getting broken things, then you're not 
doing something right.


-Justin


On Tue, Jun 14, 2016 at 10:09 AM, Justin Lemkul  wrote:




On 6/14/16 12:45 PM, Muhammad Hagras wrote:


Thanks Justin for your help,

I am also surprised from that subunit movements!

Here are the commands that I used in sequence:

1- pdb2gmx_d -f protein.pdb -o protein.gro -p protein.top
2- editconf_d -f protein.gro -o protein_pbc.gro -d 1.0
3- grompp_d -v -f minim.mdp -c protein_pbc.gro -p protein.top -o
protein.tpr
4- mdrun_d -v -deffnm protein -c protein_EM.pdb



I don't see how this sequence would lead to any issues, with or without
PBC. But in any case, for visualization purposes, just re-image using
trjconv.

-Justin


Thanks for help,


Muhammad

On Tue, Jun 14, 2016 at 4:23 AM, Justin Lemkul  wrote:




On 6/13/16 9:26 PM, Muhammad Hagras wrote:

Hi folks,


I need some help in running EM on three subunits protein (not covalently
bonded),

When I run EM on such molecule in vacuum or in implicit solvent, the
three
subunits move apart ?! I tried with and without pbc and with and without
implicit solvent and still the same results!


That seems somewhat impossible.  Without PBC, there is no box and

therefore atoms/molecules don't jump.  You're applying restraints, so
there
shouldn't be any really large movement.  "Broken" molecules are due to
PBC,
so all you're seeing is the fact that with PBC, you haven't set up the
box
appropriately.  But you haven't provided enough information (all commands
up to this point, including how you set up the box), so it's a bit of a
guess.

-Justin



Here is my minim.mdp I used

---
title   = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to
find
certain files
cpp = /lib/cpp  ; Preprocessor

; Define can be used to control processes
define  = -DPOSRES

; Parameters describing what to do, when to stop and what to save
integrator  = cg; Algorithm (steep = steepest descent
minimization)
emtol   = 10.0  ; Stop minimization when the maximum
force
< 1.0 kJ/mol
nstcalclr   = 1
nstcgsteep  = 1
dt  = 0.001
nsteps  = 10; Maximum number of
(minimization)
steps to perform
nstenergy   = 1 ; Write energies to disk every nstenergy
steps
energygrps  = System; Which energy group(s) to write to disk
;freezegrps = Backbone
;freezedim  = Y Y Y
rlist   = 1.0
lincs_order = 8
lincs_iter  = 4
nstcomm = 1
nstcalcenergy   = 1
cutoff-scheme = group

comm_mode   = Linear
;nstcomm= 1
;dispcorr   = EnerPres
;optimize_fft   = yes
;pme_order  = 6
; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions
ns_type = grid;simple   ; Method to determine neighbor list
(simple, grid)
coulombtype = PME;cut-off   ; Treatment of long range electrostatic
interactions
vdwtype = cut-off
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
;constraints= all-bonds ; Bond types to replace by
constraints
pbc = xyz   ; Periodic Boundary Conditions (yes/no)i


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = no;gbsa

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still;OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 4
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of
GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension   = 2.25936

---

Thanks for help,

Muhammad Hagras
PhD, Biophysics UCD


--

==

Re: [gmx-users] Gromacs multisubunit defragmentation

[Muhammad Hagras]

It actually worked now with the option pbc=no (I was previously just
commenting out pbc but it seems it is not the same as pbc=no!),

But with pbc=xyz, it does fragment! Weird! When playing with the box size,
I see different fragmentation patterns!

On Tue, Jun 14, 2016 at 10:09 AM, Justin Lemkul  wrote:

>
>
> On 6/14/16 12:45 PM, Muhammad Hagras wrote:
>
>> Thanks Justin for your help,
>>
>> I am also surprised from that subunit movements!
>>
>> Here are the commands that I used in sequence:
>>
>> 1- pdb2gmx_d -f protein.pdb -o protein.gro -p protein.top
>> 2- editconf_d -f protein.gro -o protein_pbc.gro -d 1.0
>> 3- grompp_d -v -f minim.mdp -c protein_pbc.gro -p protein.top -o
>> protein.tpr
>> 4- mdrun_d -v -deffnm protein -c protein_EM.pdb
>>
>>
> I don't see how this sequence would lead to any issues, with or without
> PBC. But in any case, for visualization purposes, just re-image using
> trjconv.
>
> -Justin
>
>
> Thanks for help,
>>
>> Muhammad
>>
>> On Tue, Jun 14, 2016 at 4:23 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/13/16 9:26 PM, Muhammad Hagras wrote:
>>>
>>> Hi folks,

 I need some help in running EM on three subunits protein (not covalently
 bonded),

 When I run EM on such molecule in vacuum or in implicit solvent, the
 three
 subunits move apart ?! I tried with and without pbc and with and without
 implicit solvent and still the same results!


 That seems somewhat impossible.  Without PBC, there is no box and
>>> therefore atoms/molecules don't jump.  You're applying restraints, so
>>> there
>>> shouldn't be any really large movement.  "Broken" molecules are due to
>>> PBC,
>>> so all you're seeing is the fact that with PBC, you haven't set up the
>>> box
>>> appropriately.  But you haven't provided enough information (all commands
>>> up to this point, including how you set up the box), so it's a bit of a
>>> guess.
>>>
>>> -Justin
>>>
>>>
>>>
>>> Here is my minim.mdp I used
 ---
 title   = Energy Minimization   ; Title of run

 ; The following line tell the program the standard locations where to
 find
 certain files
 cpp = /lib/cpp  ; Preprocessor

 ; Define can be used to control processes
 define  = -DPOSRES

 ; Parameters describing what to do, when to stop and what to save
 integrator  = cg; Algorithm (steep = steepest descent
 minimization)
 emtol   = 10.0  ; Stop minimization when the maximum
 force
 < 1.0 kJ/mol
 nstcalclr   = 1
 nstcgsteep  = 1
 dt  = 0.001
 nsteps  = 10; Maximum number of
 (minimization)
 steps to perform
 nstenergy   = 1 ; Write energies to disk every nstenergy
 steps
 energygrps  = System; Which energy group(s) to write to disk
 ;freezegrps = Backbone
 ;freezedim  = Y Y Y
 rlist   = 1.0
 lincs_order = 8
 lincs_iter  = 4
 nstcomm = 1
 nstcalcenergy   = 1
 cutoff-scheme = group

 comm_mode   = Linear
 ;nstcomm= 1
 ;dispcorr   = EnerPres
 ;optimize_fft   = yes
 ;pme_order  = 6
 ; Parameters describing how to find the neighbors of each atom and how
 to
 calculate the interactions
 ns_type = grid;simple   ; Method to determine neighbor list
 (simple, grid)
 coulombtype = PME;cut-off   ; Treatment of long range electrostatic
 interactions
 vdwtype = cut-off
 rcoulomb= 1.0   ; long range electrostatic cut-off
 rvdw= 1.0   ; long range Van der Waals cut-off
 ;constraints= all-bonds ; Bond types to replace by
 constraints
 pbc = xyz   ; Periodic Boundary Conditions (yes/no)i


 ; IMPLICIT SOLVENT ALGORITHM
 implicit_solvent = no;gbsa

 ; GENERALIZED BORN ELECTROSTATICS
 ; Algorithm for calculating Born radii
 gb_algorithm = Still;OBC
 ; Frequency of calculating the Born radii inside rlist
 nstgbradii   = 1
 ; Cutoff for Born radii calculation; the contribution from atoms
 ; between rlist and rgbradii is updated every nstlist steps
 rgbradii = 1.0
 ; Dielectric coefficient of the implicit solvent
 gb_epsilon_solvent   = 4
 ; Salt concentration in M for Generalized Born models
 gb_saltconc  = 0
 ; Scaling factors used in the OBC GB model. Default values are OBC(II)
 gb_obc_alpha = 1
 gb_obc_beta  = 0.8
 gb_obc_gamma = 4.85
 gb_dielectric_offset = 0.009
 sa_algorithm = Ace-approximation
 ; Surface tension (kJ/mol/nm^2) for the SA 

Re: [gmx-users] Gromacs multisubunit defragmentation

[Justin Lemkul]

On 6/14/16 12:45 PM, Muhammad Hagras wrote:

Thanks Justin for your help,

I am also surprised from that subunit movements!

Here are the commands that I used in sequence:

1- pdb2gmx_d -f protein.pdb -o protein.gro -p protein.top
2- editconf_d -f protein.gro -o protein_pbc.gro -d 1.0
3- grompp_d -v -f minim.mdp -c protein_pbc.gro -p protein.top -o protein.tpr
4- mdrun_d -v -deffnm protein -c protein_EM.pdb



I don't see how this sequence would lead to any issues, with or without PBC. 
But in any case, for visualization purposes, just re-image using trjconv.


-Justin


Thanks for help,

Muhammad

On Tue, Jun 14, 2016 at 4:23 AM, Justin Lemkul  wrote:




On 6/13/16 9:26 PM, Muhammad Hagras wrote:


Hi folks,

I need some help in running EM on three subunits protein (not covalently
bonded),

When I run EM on such molecule in vacuum or in implicit solvent, the three
subunits move apart ?! I tried with and without pbc and with and without
implicit solvent and still the same results!



That seems somewhat impossible.  Without PBC, there is no box and
therefore atoms/molecules don't jump.  You're applying restraints, so there
shouldn't be any really large movement.  "Broken" molecules are due to PBC,
so all you're seeing is the fact that with PBC, you haven't set up the box
appropriately.  But you haven't provided enough information (all commands
up to this point, including how you set up the box), so it's a bit of a
guess.

-Justin




Here is my minim.mdp I used
---
title   = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp = /lib/cpp  ; Preprocessor

; Define can be used to control processes
define  = -DPOSRES

; Parameters describing what to do, when to stop and what to save
integrator  = cg; Algorithm (steep = steepest descent
minimization)
emtol   = 10.0  ; Stop minimization when the maximum force
< 1.0 kJ/mol
nstcalclr   = 1
nstcgsteep  = 1
dt  = 0.001
nsteps  = 10; Maximum number of (minimization)
steps to perform
nstenergy   = 1 ; Write energies to disk every nstenergy
steps
energygrps  = System; Which energy group(s) to write to disk
;freezegrps = Backbone
;freezedim  = Y Y Y
rlist   = 1.0
lincs_order = 8
lincs_iter  = 4
nstcomm = 1
nstcalcenergy   = 1
cutoff-scheme = group

comm_mode   = Linear
;nstcomm= 1
;dispcorr   = EnerPres
;optimize_fft   = yes
;pme_order  = 6
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type = grid;simple   ; Method to determine neighbor list
(simple, grid)
coulombtype = PME;cut-off   ; Treatment of long range electrostatic
interactions
vdwtype = cut-off
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
;constraints= all-bonds ; Bond types to replace by
constraints
pbc = xyz   ; Periodic Boundary Conditions (yes/no)i


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = no;gbsa

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still;OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 4
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension   = 2.25936

---

Thanks for help,

Muhammad Hagras
PhD, Biophysics UCD



--
==

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] Simple gas-phase minimization help

[Justin Lemkul]

On 6/14/16 1:02 PM, Tarick E wrote:

Hey everyone,

I am new to this, so please forgive me if this has been asked before.

I am trying to conduct an energy minimization in vacuum on individual
proteins and small peptides at a constant temperature, but I am having


There is no temperature during energy minimization.


trouble with this. Is there any documentation someone can lead me to for
producing a vacuum-phase minimization .mdp file? I have been trying to edit
the various .mdp files provided in the Lysozyme tutorial written by Justin
Lemkul, but I haven't had any luck and I can't seem to locate any info in
the Gromacs users manual.



Set all cutoffs to zero and do not use PBC.  Then you're in vacuum.

-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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Simple gas-phase minimization help

[Tarick E]

Hey everyone,

I am new to this, so please forgive me if this has been asked before.

I am trying to conduct an energy minimization in vacuum on individual
proteins and small peptides at a constant temperature, but I am having
trouble with this. Is there any documentation someone can lead me to for
producing a vacuum-phase minimization .mdp file? I have been trying to edit
the various .mdp files provided in the Lysozyme tutorial written by Justin
Lemkul, but I haven't had any luck and I can't seem to locate any info in
the Gromacs users manual.

Thanks!

Sincerely,

Tarick El-Baba
Indiana University
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Re: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

[Christopher Neale]

How long are your simulations? I build a DPPC bilayer with charmm-GUI and 
simulate for 300 ns at 323 K and the APL has a mean of 0.61 nm^2 and a standard 
deviation of 0.01 nm^2. However, the APL does happen to dip down to 0.59 within 
10 ns... it's just that the fluctuations will also sometimes take it as high as 
0.65 and as low as 0.57. Maybe give us your simulation time and upload a plot 
of APL vs. time and post the link here (no direct attachments please). If 
you're running 10-20 ns and you see the APL get low then you may simply need to 
run for longer.

Here is the data from my simulation of DPPC at 323K:
https://www.dropbox.com/s/adu4ft8dhuyc9c2/dppc_323k_apl.pdf?dl=0

I suggest you figure things out with DPPC before moving on to your PA lipids.

Chris.


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

Sent: 13 June 2016 19:32:47
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

Hello everyone,

I have also given below the map file that I have used for equilibration.

integrator = md
dt = 0.002
nsteps = 200
nstlog = 1000
nstxout = 5000
nstvout = 1000
nstfout = 1000
nstcalcenergy = 100
nstxtcout   = 1000
nstenergy = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
;
tcoupl = Nose-Hoover
tc_grps = MEMB SOL_ION
tau_t = 1.0 1.0
ref_t = 323.15 323.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = MEMB SOL_ION
;
refcoord_scaling = com


Thanks,

Nidhin Thomas
University of Houston

> Message: 4
> Date: Mon, 13 Jun 2016 17:51:43 +
> From: Christopher Neale 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>   , "gmx-us...@gromacs.org"
>   
> Subject: Re: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer
>   obtainedfrom CHARMM-GUI
> Message-ID:
>   
> 
>
> Content-Type: text/plain; charset="Windows-1252"
>
> In future posts, it is best to copy and paste your .mdp file because we can 
> not all get attachments from the list.
>
> Regarding your results, it is my understanding that the CHARMM-GUI has 
> parameters for, and can build, many lipids systems whose parameters have not 
> been completely validated by simulations in the literature (e.g. for things 
> like APL). Last time I looked, PG was the only anionic charmm36 lipid that 
> was shown to behave properly in bilayers (Klauda), though others may have 
> since been shown to work well.
>
> If the issue is not simply that the PA parameters are not very good, then one 
> likely source of problem is that perhaps you are not using the NBfix ions? 
> That could be a big deal. I never use Na with membranes for this reason, so 
> you could try KCl instead.
>
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Nidhin 
> Thomas 
> Sent: 12 June 2016 18:38:43
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained  
>   from CHARMM-GUI
>
> Hello GROMACS Users,
>
> I have modelled a mixed bilayer system consisting of 35 DPPC lipids and one 
> POPA lipid (in each monolayers) using CHARMM-GUI. NPT ensemble was chosen 
> while creating the model. TIP3 water model was used for modeling. I did not 
> use surface tension for the membrane.
>
> I have simulated the system for 50 nanoseconds now. I have noticed that 
> average area per lipid of the system is only 58.55 Angstrom2. I saw from 
> literature that it should be around 63 and even at CHARMM-GUI, it is 
> mentioned as 63 while creating the bilayer.
>
> I have used the exact .mdp files given by CHARMM-GUI for minimization, 
> equilibration and production run.
>
> Can anyone please help me identify what could have possibly gone wrong in my 
> simulation? I have attached the .mdp file used for production run and 
> equilibration here for reference.
>
> In addition, I keep on getting these NOTES while running the grompp command 
> prior to mdrun before it creates a .tpr file. I don?t know if this has got 
> something to do with the simulation.
>
> NOTE 1 [file step7_production_2.mdp]:
>  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
> Estimate for the relative computational load of the PME mesh part: 0.05
> Excluding 2 

Re: [gmx-users] Gromacs multisubunit defragmentation

[Muhammad Hagras]

Thanks Justin for your help,

I am also surprised from that subunit movements!

Here are the commands that I used in sequence:

1- pdb2gmx_d -f protein.pdb -o protein.gro -p protein.top
2- editconf_d -f protein.gro -o protein_pbc.gro -d 1.0
3- grompp_d -v -f minim.mdp -c protein_pbc.gro -p protein.top -o protein.tpr
4- mdrun_d -v -deffnm protein -c protein_EM.pdb

Thanks for help,

Muhammad

On Tue, Jun 14, 2016 at 4:23 AM, Justin Lemkul  wrote:

>
>
> On 6/13/16 9:26 PM, Muhammad Hagras wrote:
>
>> Hi folks,
>>
>> I need some help in running EM on three subunits protein (not covalently
>> bonded),
>>
>> When I run EM on such molecule in vacuum or in implicit solvent, the three
>> subunits move apart ?! I tried with and without pbc and with and without
>> implicit solvent and still the same results!
>>
>>
> That seems somewhat impossible.  Without PBC, there is no box and
> therefore atoms/molecules don't jump.  You're applying restraints, so there
> shouldn't be any really large movement.  "Broken" molecules are due to PBC,
> so all you're seeing is the fact that with PBC, you haven't set up the box
> appropriately.  But you haven't provided enough information (all commands
> up to this point, including how you set up the box), so it's a bit of a
> guess.
>
> -Justin
>
>
>
>> Here is my minim.mdp I used
>> ---
>> title   = Energy Minimization   ; Title of run
>>
>> ; The following line tell the program the standard locations where to find
>> certain files
>> cpp = /lib/cpp  ; Preprocessor
>>
>> ; Define can be used to control processes
>> define  = -DPOSRES
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator  = cg; Algorithm (steep = steepest descent
>> minimization)
>> emtol   = 10.0  ; Stop minimization when the maximum force
>> < 1.0 kJ/mol
>> nstcalclr   = 1
>> nstcgsteep  = 1
>> dt  = 0.001
>> nsteps  = 10; Maximum number of (minimization)
>> steps to perform
>> nstenergy   = 1 ; Write energies to disk every nstenergy
>> steps
>> energygrps  = System; Which energy group(s) to write to disk
>> ;freezegrps = Backbone
>> ;freezedim  = Y Y Y
>> rlist   = 1.0
>> lincs_order = 8
>> lincs_iter  = 4
>> nstcomm = 1
>> nstcalcenergy   = 1
>> cutoff-scheme = group
>>
>> comm_mode   = Linear
>> ;nstcomm= 1
>> ;dispcorr   = EnerPres
>> ;optimize_fft   = yes
>> ;pme_order  = 6
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> ns_type = grid;simple   ; Method to determine neighbor list
>> (simple, grid)
>> coulombtype = PME;cut-off   ; Treatment of long range electrostatic
>> interactions
>> vdwtype = cut-off
>> rcoulomb= 1.0   ; long range electrostatic cut-off
>> rvdw= 1.0   ; long range Van der Waals cut-off
>> ;constraints= all-bonds ; Bond types to replace by
>> constraints
>> pbc = xyz   ; Periodic Boundary Conditions (yes/no)i
>>
>>
>> ; IMPLICIT SOLVENT ALGORITHM
>> implicit_solvent = no;gbsa
>>
>> ; GENERALIZED BORN ELECTROSTATICS
>> ; Algorithm for calculating Born radii
>> gb_algorithm = Still;OBC
>> ; Frequency of calculating the Born radii inside rlist
>> nstgbradii   = 1
>> ; Cutoff for Born radii calculation; the contribution from atoms
>> ; between rlist and rgbradii is updated every nstlist steps
>> rgbradii = 1.0
>> ; Dielectric coefficient of the implicit solvent
>> gb_epsilon_solvent   = 4
>> ; Salt concentration in M for Generalized Born models
>> gb_saltconc  = 0
>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>> gb_obc_alpha = 1
>> gb_obc_beta  = 0.8
>> gb_obc_gamma = 4.85
>> gb_dielectric_offset = 0.009
>> sa_algorithm = Ace-approximation
>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>> sa_surface_tension   = 2.25936
>>
>> ---
>>
>> Thanks for help,
>>
>> Muhammad Hagras
>> PhD, Biophysics UCD
>>
>>
> --
> ==
>
> 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
> 

Re: [gmx-users] Non-neutral system with iron-sulfur clusters

[Justin Lemkul]

On 6/14/16 7:37 AM, Marlon Sidore wrote:

I checked everything and even by adding the numbers on the paper and the
cystein charges from amber03 (the FF they used in the paper) the resulting
charge isn't an integer.

The paper has charges for the Fe (4x), the S (4x) from the cluster, the S
from the CYS bound to it and the CB bound to the previous S in CYS. Simply
adding them and the other atoms from CYS (4x in case of the CYS atoms)
doesn't yield an integer. I didn't count S and CB twice either.

The resulting charge from the whole 4CYS-4Fe-4S is -1.233684.



You should contact the corresponding author of the paper.  This is not a GROMACS 
problem.


-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] Non-neutral system with iron-sulfur clusters

[Marlon Sidore]

I checked everything and even by adding the numbers on the paper and the
cystein charges from amber03 (the FF they used in the paper) the resulting
charge isn't an integer.

The paper has charges for the Fe (4x), the S (4x) from the cluster, the S
from the CYS bound to it and the CB bound to the previous S in CYS. Simply
adding them and the other atoms from CYS (4x in case of the CYS atoms)
doesn't yield an integer. I didn't count S and CB twice either.

The resulting charge from the whole 4CYS-4Fe-4S is -1.233684.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-14 13:20 GMT+02:00 Justin Lemkul :

>
>
> On 6/14/16 4:59 AM, Marlon Sidore wrote:
>
>> Hello everyone,
>>
>> On my quest to use the parameters for iron-sulfur clusters from [1] I
>> realized that the resulting clusters are not neutral. Indeed, even though
>> the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
>> of the cluster + the 4 CYS isn't a round number.
>>
>> Should I worry ?
>>
>>
> Non-integer charges are totally non-physical, so using such a topology
> would be wrong.  Check carefully that you've assigned everything correctly.
>
> -Justin
>
> 1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
>> C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase.
>> J.
>> Chem. Theory Comput. 8, 2103–2114 (2012).
>>
>> Marlon Sidore
>>
>>
>> PhD Student
>> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
>> CNRS - UMR7255
>> 31, Chemin Joseph Aiguier
>> 13402 cedex 20 Marseille
>> France
>>
>>
> --
> ==
>
> 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
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> * Please search the archive at
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> posting!
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Re: [gmx-users] Gromacs multisubunit defragmentation

[Justin Lemkul]

On 6/13/16 9:26 PM, Muhammad Hagras wrote:

Hi folks,

I need some help in running EM on three subunits protein (not covalently
bonded),

When I run EM on such molecule in vacuum or in implicit solvent, the three
subunits move apart ?! I tried with and without pbc and with and without
implicit solvent and still the same results!



That seems somewhat impossible.  Without PBC, there is no box and therefore 
atoms/molecules don't jump.  You're applying restraints, so there shouldn't be 
any really large movement.  "Broken" molecules are due to PBC, so all you're 
seeing is the fact that with PBC, you haven't set up the box appropriately.  But 
you haven't provided enough information (all commands up to this point, 
including how you set up the box), so it's a bit of a guess.


-Justin



Here is my minim.mdp I used
---
title   = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp = /lib/cpp  ; Preprocessor

; Define can be used to control processes
define  = -DPOSRES

; Parameters describing what to do, when to stop and what to save
integrator  = cg; Algorithm (steep = steepest descent
minimization)
emtol   = 10.0  ; Stop minimization when the maximum force
< 1.0 kJ/mol
nstcalclr   = 1
nstcgsteep  = 1
dt  = 0.001
nsteps  = 10; Maximum number of (minimization)
steps to perform
nstenergy   = 1 ; Write energies to disk every nstenergy
steps
energygrps  = System; Which energy group(s) to write to disk
;freezegrps = Backbone
;freezedim  = Y Y Y
rlist   = 1.0
lincs_order = 8
lincs_iter  = 4
nstcomm = 1
nstcalcenergy   = 1
cutoff-scheme = group

comm_mode   = Linear
;nstcomm= 1
;dispcorr   = EnerPres
;optimize_fft   = yes
;pme_order  = 6
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type = grid;simple   ; Method to determine neighbor list
(simple, grid)
coulombtype = PME;cut-off   ; Treatment of long range electrostatic
interactions
vdwtype = cut-off
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
;constraints= all-bonds ; Bond types to replace by
constraints
pbc = xyz   ; Periodic Boundary Conditions (yes/no)i


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = no;gbsa

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still;OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 4
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension   = 2.25936

---

Thanks for help,

Muhammad Hagras
PhD, Biophysics UCD



--
==

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] (no subject)

[Justin Lemkul]

On 6/14/16 4:38 AM, Sepideh Momeninezhad wrote:

hello everyone,i want to know how can i make average structure for my
molecule?



gmx rmsf -ox

Whether or not an average structure is at all meaningful or physical is another 
matter. http://www.gromacs.org/Documentation/Terminology/Average_Structure


-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] Non-neutral system with iron-sulfur clusters

[Justin Lemkul]

On 6/14/16 4:59 AM, Marlon Sidore wrote:

Hello everyone,

On my quest to use the parameters for iron-sulfur clusters from [1] I
realized that the resulting clusters are not neutral. Indeed, even though
the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
of the cluster + the 4 CYS isn't a round number.

Should I worry ?



Non-integer charges are totally non-physical, so using such a topology would be 
wrong.  Check carefully that you've assigned everything correctly.


-Justin


1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. J.
Chem. Theory Comput. 8, 2103–2114 (2012).

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France



--
==

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] (no subject)

[Sarath Chandra]

For analyzing nucleic acid structural properties with gromacs files you can
try out

https://github.com/rjdkmr/do_x3dna

or x3dna (which works on single pdb files, do_x3dna calls x3dna functions
but works on the entire trajectory) or curve or NAFlex (
http://mmb.irbbarcelona.org/NAFlex/)

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 14 June 2016 at 15:13, Sepideh Momeninezhad <
sepideh.momeninez...@gmail.com> wrote:

> dear gromacs users who know a little about curve?i want to use it for a
> peptide nucleic acid and i do not know how i should modify it?
> --
> Gromacs Users mailing list
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Re: [gmx-users] How to run gromacs on gpu?

[Catarina A. Carvalheda dos Santos]

Hi Shahab,

Maybe check GROMACS documentation -->
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc

Cheers,

On 14 June 2016 at 10:42, shahab shariati  wrote:

> Dear all,
>
> How to run gromacs on gpu?
>
> Which command is required? mdrun? Which options?
>
> Best,
> Shahab
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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[gmx-users] (no subject)

[Sepideh Momeninezhad]

dear gromacs users who know a little about curve?i want to use it for a
peptide nucleic acid and i do not know how i should modify it?
-- 
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[gmx-users] How to run gromacs on gpu?

[shahab shariati]

Dear all,

How to run gromacs on gpu?

Which command is required? mdrun? Which options?

Best,
Shahab
-- 
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[gmx-users] Non-neutral system with iron-sulfur clusters

[Marlon Sidore]

Hello everyone,

On my quest to use the parameters for iron-sulfur clusters from [1] I
realized that the resulting clusters are not neutral. Indeed, even though
the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
of the cluster + the 4 CYS isn't a round number.

Should I worry ?

1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. J.
Chem. Theory Comput. 8, 2103–2114 (2012).

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France
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[gmx-users] (no subject)

[Sepideh Momeninezhad]

hello everyone,i want to know how can i make average structure for my
molecule?
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Re: [gmx-users] interfacing with Gaussian 09

[Groenhof, Gerrit]

Hi,

>From the gromacs side it seems to work fine. That the 
>GMX_QM_MODIFIED_LINKS_DIR needs to be set is that gromacs still expect them, 
>but when you use the script it does not need them.

If you inspect the script you'll see that it does nothing more than copy the 
input file created by gromacs into a temp.com, run gaussian with that file and 
extracts from the default temp.log file the energy and gradients on both QM and 
MM atoms into a fort.7 file, which gromacs reads in to add these informations 
to the force and energy arrays.

>From the stderr messages tells you that you have made modifications in the 
>script that are faulty at line 18:

/fslhome/crk9/gromacs//gau: line 18: export: `/fslhome/crk9/gromacs/': not a 
valid identifier

my guess is you're mixing csh and bash languange. note that the gau script is a 
bash script

Best,

Gerrit




Gerrit,

Thanks for your suggestions. I am using GROMACS 5.1.2.

After reading through your message, I realized that I was using GAUSS_DIR
and GAUSS_EXE for the location and name of the gau script instead of
GMX_QM_GAUSS_DIR and GMX_QM_GAUSS_EXE. So I changed that, and then I got
the error message from line 227 of qm_gaussian.c : "no
$GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside."

I thought that one could use the gau script successfully without modifying
any Gaussian links.

I decided to try setting the GMX_QM_MODIFIED_LINKS_DIR environmental
variable to an empty folder. I am attaching the resulting output (as links
at the end of this message); both what was sent to stdout as well as the
gmx generated log file.

Looking through qm_gaussian.c, as well as the output I have so far, it
appears that modified Gaussian links *are* required for gmx to interface
with Gaussian.

So, the bottom line is that in order for Gromacs to interface with Gaussian
to perform a quantum molecular dynamics computation, I must have access to
the Gaussian source code. Is that correct?

https://drive.google.com/file/d/0B-W4G39j_Icjc21TcTN1S2M0MVk/view?usp=sharing
https://drive.google.com/file/d/0B-W4G39j_IcjZlVPb1NySkUtRDQ/view?usp=sharing

(Please let me know if the links above don't work.)

Thanks for your help

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University


> Message: 2
> Date: Sun, 12 Jun 2016 05:16:13 +
> From: "Groenhof, Gerrit" 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: Re: [gmx-users] interfacing with Gaussian 09 (Mark Abraham)
> Message-ID:
> <858a7947bc0fe04da05e1786a6d51d45263d6...@um-excdag-a05.um.gwdg.de
> >
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Which version of Gmx are you using?
>
> I ask because of a recent bug fix. The bug was that I tried to print the
> value of an environment variable, without checking if that variable was
> set, causing set faulting.
>
> Make sure the GMX_QM_GAUSS_DIR (for Gmx < 5 GAUSS_DIR) are set and point
> to the location of the g09 directory.
>
> IN any case, for normal gaussian runs, the program should not write out
> the LJ.dat. IF the above does not help, you could perhaps send me the input
> (off list) and I can have a look at what goes wrong.
>
> Best,
>
> Gerrit
>
>
>
> Hi,
>
> Please don't subscribe to a digest if you're planning to reply to the
> digest and de-thread the discussion. Gerrit said the other week that gau
> works.
>
> Mark
>
> On Fri, 10 Jun 2016 18:18 Mark Abraham  wrote:
>
> > Hi,
> >
> > Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and
> >
> http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
> >
> > Mark
> >
> > On Fri, Jun 10, 2016 at 5:13 PM Clinton King  >
> > wrote:
> >
> >> I'm having difficulty interfacing GROMACS with Gaussian 09. Is there
> >> anyone
> >> who has successfully done it who is willing to give some advice?
> >>
> >> --
> >> Clinton King
> >> Graduate Student
> >> Chemistry Department
> >> Brigham Young University
> >> --
> >> Gromacs Users mailing list
> >>
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