Re: [gmx-users] Neutralizing

[Parham Jabbarzadeh (Department of Biomedical Science)]

Dear Sir

Use this command:

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral

In this case, you don't need ​the number of ions​.

Kind Regards

Parham J. K.

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On Tue, Mar 8, 2016 at 3:32 PM, mohammad r  wrote:

> Hi everybody, I’ve generated a water-peptide system, now I want to
> neutralize it. Is adding adequate number of ions sufficient for
> neutralizing process or I should do QM/MM simulation for the this
> process? Thank you, Mohammad.
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[gmx-users] Neutralizing

[mohammad r]

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize 
it. Is adding adequate number of ions sufficient for neutralizing process or I 
should do QM/MM simulation for the this process? Thank you, Mohammad.
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Re: [gmx-users] query on plotting dynamical quantity

[Tsjerk Wassenaar]

Hi Jagannath,

Convert the file to PDB format and write the values to the b-factor field.
Most visualization programs can color by b-value.

Cheers,

Tsjerk
On Mar 8, 2016 06:50, "Jagannath Mondal"  wrote:

> Dear gromacs-users
>
>   I am sorry to write you a visualization-related query. I hope you can
> help.
>
> My query is: How can I visualize a trajectory file ( example in vmd)  where
> I have an extra 4th column ( apart from x y z which are first 3 columns)
> which has a dynamically changing variable for each particles ? The plan is
> to color gradient the atoms using the values of   4th column.
>
>
> Is there a way to do it. I am sorry again to write you off the list.
>  Here is an excerpt from first few lines:
> Jagannath
>
>219GLN  C  186.961000 4.468000 3.7760001.678980
>
> 220LEU  C  376.753000 4.257000 3.98  6.526284
>
> 221THR  C  516.618000 4.023000 4.151000  11.323132
>
> 222ALA  C  616.565000 3.742000 4.306000  26.957896
>
> 223ALA  C  716.409000 3.464000 4.313000  52.708403
>
> 224GLN  C  886.213000 3.54 4.528000
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[gmx-users] query on plotting dynamical quantity

[Jagannath Mondal]

Dear gromacs-users

  I am sorry to write you a visualization-related query. I hope you can
help.

My query is: How can I visualize a trajectory file ( example in vmd)  where
I have an extra 4th column ( apart from x y z which are first 3 columns)
which has a dynamically changing variable for each particles ? The plan is
to color gradient the atoms using the values of   4th column.


Is there a way to do it. I am sorry again to write you off the list.
 Here is an excerpt from first few lines:
Jagannath

   219GLN  C  186.961000 4.468000 3.7760001.678980

220LEU  C  376.753000 4.257000 3.98  6.526284

221THR  C  516.618000 4.023000 4.151000  11.323132

222ALA  C  616.565000 3.742000 4.306000  26.957896

223ALA  C  716.409000 3.464000 4.313000  52.708403

224GLN  C  886.213000 3.54 4.528000
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[gmx-users] distance restraints in mdp

[Sana Saeed]

i am performing protein ligand binding free energy calculation MD. i have 
applied distance restraint to 1 pair of atoms. now when i am running md it 
gives me LINCS warnings. first i thought it is because of wrong geometry so i 
changed complex, now i am doing it for Lysozyme+JZ4. but still same warning. i 
am confused about the distance restraints to be introduced in mdp file. disre = 
simple/ensemble? i read in manual, but still confused. i tried both with 
"simple it gives me LINCS warning and with ensemble it says that this version 
of gromacs doesnt support it. i am using 5.1 gromacs. Sana Saeed Khan,
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[gmx-users] TIP5P and crystal waters

[Irem Altan]

Hi,

I am trying to run a simulation with TIP5P and Gromacs 5.1.2. I want to do so 
by keeping the crystal waters in the .pdb file. When I don’t erase the crystal 
waters and run pdb2gmx, I get the following error:

Fatal error:
Residue 'HO5' not found in residue topology database

This error disappears when I remove crystal waters. Why does this happen? How 
can I keep the crystal waters?
(Note that this is an issue only with TIP5P and other water models work without 
a problem)

Best,
Irem
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[gmx-users] Regression test 4.6.7

[Nicolas Cheron]

Dear all,

I am looking for the file regressiontests-4.6.7.tar.gz. I can't find it
online, the previous links are done. Can someone please either send it to
me or tell me where to find it?

Thanks a lot.

Nicolas
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Re: [gmx-users] problem with water models in Gromacs 5.1.2

[Irem Altan]

Hi,

Yes, the tests were performed. It turns out that I had to reduce the energy 
step size during minimization. Thank you.

Best,
Irem

> On Mar 6, 2016, at 11:27 AM, Justin Lemkul  wrote:
> 
> 
> 
> On 3/4/16 4:04 PM, Irem Altan wrote:
>> Hi,
>> 
>> It turns out that my problems with TIP5P were more general than I thought. I 
>> recently switched from version 4.6.5, with which I could run simulations 
>> using AMBER99SB + (SPC, SPC/E, TIP4P, TIP3P). I decided to do the following 
>> test:
>> 
>> 1- I created a .pdb file with a single calcium ion, within a cubic unit cell 
>> of side 30 A:
>> 
>> (test.pdb)
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
>> HETATM1 CACA A 132.702 -10.496  -5.429  1.00 12.22  
>> CA
>> 
>> 2- I then run pdb2gmx and select amber99sb and SPC (I tried it with TIP4P as 
>> well):
>> 
>> gmx pdb2gmx -f test.pdb -o box.gro -p topol.top
>> 
>> 3- I run solvate:
>> 
>> gmx solvate -cp box.gro -cs spc216 -p topol.top -o box_h2o.gro
>> 
>> 4- then I substitute some waters with sodium and chloride ions:
>> 
>> gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
>> gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05
>> 
>> 5- Energy minimization (this is where things go horribly wrong):
>> 
>> gmx grompp -f minim.mdp -p topol.top -c ions.gro -o em.tpr
>> gmx mdrun -v -deffnm em
>> 
>> Then the following error appears:
>> 
>> Fatal error:
>> 
>> step 11: Water molecule starting at atom 86 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> 
>> I’m guessing there is something that changed from version 4.6.5 to 5.1.2 
>> that I can’t pinpoint. What could I be overlooking? (The contents of my .mdp 
>> files are below)
>> 
> 
> Do the regression tests pass on your installation?  A box of water and ions 
> should not fail in any GROMACS version, ever.
> 
> -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] Regarding error while generating topology for protein

[Justin Lemkul]

On 3/7/16 6:31 AM, shrikant kaushik wrote:

hello sir,
   I have query related to topology file generation for my protein, THR
residue is Phosphorylated  (TPO), it showing error while running pdbtogmx.
how to generate topology file for protein along with TPO residue.



http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Many force fields support phosphorylated residues, you need to use one that 
does.

-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] Extending the simulation

[sun]

Yes I have done it now. Thank you so much guys. 

Sent from my iPhone

> On 07-Mar-2016, at 4:32 pm, jkrie...@mrc-lmb.cam.ac.uk wrote:
> 
> This page is now a little out of date. GROMACS 5 has replaced tbpconv with
> gmx convert-tpr but otherwise the instructions are the same.
> 
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>> 
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> 
> 
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Re: [gmx-users] GROMOS force field for sphingomyelin and cholesterol

[Piggot T.]

You need to be a bit more specific. What other lipids do you have in the 
membrane and which force field are you/do you want to use for these (and I mean 
more than just GROMOS, but exactly which parameters they are e.g. 43A1-S3, 
53A6L, etc.).

There are some GROMOS compatible force fields out there for 
cholesterol/sphingomyelin but the choice will also depend upon which other 
lipids you have in your systems (as everything needs to be compatible in the 
system).

Cheers

Tom

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 凌未风 
[grx1...@qq.com]
Sent: 07 March 2016 05:08
To: gromacs.org_gmx-users
Subject: [gmx-users] GROMOS force field for sphingomyelin and cholesterol

Hello everyone:

I am planning to do some simulation of bilayer mixtures (maybe also include 
protein). I am planning to include sphingomyelin and cholesterol in my system. 
Could anyone let me know where to get the gromos force filed for these two 
molecules (I am using gromos force field for some reasons)?

Thanks very much.

Cheers,
RXG
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Re: [gmx-users] Extending the simulation

[jkrieger]

This page is now a little out of date. GROMACS 5 has replaced tbpconv with
gmx convert-tpr but otherwise the instructions are the same.

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
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Re: [gmx-users] Extending the simulation

[Sun Iba]

Thank you very much.

Regards
Suniba

On Mon, Mar 7, 2016 at 10:09 AM, Nikhil Maroli  wrote:

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
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