[gmx-users] Distance restraint between two chains' com

[WT Ren]

Dear Gromacs Users,

I am trying to apply a distance restraint between two chains' center of
mass to  prevent them diffusing far away from each other. As I known, the
pull code seems only can restrain the distance to a reference distance with
 harmonic potential, while the distance restraint seems can not be applied
to center of mass.

So can anyone help on this issue?

Best regards

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn *
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[gmx-users] Distance restraint between two chains' com

[WT Ren]

Dear Gromacs Users,

I am trying to apply a distance restraint between two chains' center of
mass to  prevent them diffusing far away from each other. As I known, the
pull code seems only can restrain the distance to a reference distance with
 harmonic potential, while the distance restraint seems can not be applied
to center of mass.

So can anyone help on this issue?

Best regards

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn *
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 130, Issue 12

[Xia, Xiaole]

Hi Justin,
Yes, it seems I trashed the .xtc files and I have run my binary files through 
it. How to recover it? Thanks!

Jerry

Message: 5
Date: Wed, 04 Feb 2015 21:00:54 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to recover the .xtc from wrong operation
'dos2unix'
Message-ID: <54d2ced6.4030...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 2/4/15 8:09 PM, Xia, Xiaole wrote:
> Hi,
> I just use dos2unix to change the .xtc, and system will say 'floating point 
> exception' when I want to analysis it. Is there any method to recover it or 
> how to solve this problem? I use the same version of gromacs and analysis on 
> odessay. And the old one still works which was not changed by dos2unix. Some 
> my .trr were deleted. Thanks!

You've probably trashed the files by using dos2unix, which is only intended for
fixing line endings in text files.  Don't run your binary files through it.

-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] Umbrella Samling Alteration

[Alexander Law]

Hi Justin

The runs have started but they are not currently running, as in they were 
cancelled and I can start them up again using the .cpt file. Is it still 
possible to alter add the -nsteps in this case?

Many Thanks,
Alex

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Tuesday, February 03, 2015 1:51 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Samling Alteration

On 2/1/15 11:22 PM, Alexander Law wrote:
> Dear Gromacs Users
>
> I am currently running the series of simulations using the following command:
>
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>
> I wish to lessen the amount of time for each of these simulations from 10 ns 
> to 6 ns. These simulations are already up to around 5 ns, is it possible to 
> change the time to 6 ns without altering the md_umbrella.mdp file and 
> starting agin? Also, will this reduction have any major impacts on the 
> quality/efficacy of the data?
>

Use mdrun command-line option -nsteps to override the number of steps specified
in the .tpr file, but you can't do this if the runs are in progress.

-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 recover the .xtc from wrong operation 'dos2unix'

[Justin Lemkul]

On 2/4/15 8:09 PM, Xia, Xiaole wrote:

Hi,
I just use dos2unix to change the .xtc, and system will say 'floating point 
exception' when I want to analysis it. Is there any method to recover it or how 
to solve this problem? I use the same version of gromacs and analysis on 
odessay. And the old one still works which was not changed by dos2unix. Some my 
.trr were deleted. Thanks!


You've probably trashed the files by using dos2unix, which is only intended for 
fixing line endings in text files.  Don't run your binary files through it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] How to recover the .xtc from wrong operation 'dos2unix'

[Xia, Xiaole]

Hi,
I just use dos2unix to change the .xtc, and system will say 'floating point 
exception' when I want to analysis it. Is there any method to recover it or how 
to solve this problem? I use the same version of gromacs and analysis on 
odessay. And the old one still works which was not changed by dos2unix. Some my 
.trr were deleted. Thanks!
Best!

Jerry Xia
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Re: [gmx-users] adding polyatomic species in water

[Kester Wong]

Check whether the configuration of the atom with highest force is configured reasonably.If you are only getting a few minimisation steps before crashing, then perhaps minimising your cell using a double precision GROMACS would help?Cheers,Kester- 원본 메일 -보낸사람 : #SUKRITI GUPTA# 받는사람 : "gmx-us...@gromacs.org" 받은날짜 : 2015년 2월 4일(수) 19:10:26제목 : [gmx-users] adding polyatomic species in waterDear Gromacs Users,


I am trying to simulate a cell containing different polyatomic species like sulphate, glucose, acetic acid etc. in water. I start my simulation by taking pdb file containing 1 sulphate ion and then add remaining sulphate ions and other species using -cs and -ci from genbox. I use genbox command multiple time till all the species are added and system is solvated in water. But when I perform energy minimisation, the initial system starts with a very high energy i.e. around 10^6 range and the either it doesn't get converged or i get msg Segmentation fault (core dumped).


I also tried using genconf but still i was getting the same problem.


Can anyone please let me know what is wrong with my system and how can i correctly add all the species in my system.


Regards

Sukriti


[https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif]

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg


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Re: [gmx-users] Peptide-membrane simulation force field parameters

[Justin Lemkul]

On 2/4/15 2:28 AM, tarak karmakar wrote:

Dear All,
I need a suggestion related to simulation of peptide-membrane system.
Are CGenFF parameters (from ParamChem) for peptide analogues good enough to
couple with Charmm36 parameters for the lipids in a membrane? (provided
very low charge and param penalties)



The protein force field is highly optimized, and we generally recommend against 
trying to shoehorn CGenFF parameters into it.  Low penalties just indicate that 
we cover the chemical space reasonably well in the force field, but that's not 
necessarily an indicator that those parameters will properly represent a protein 
moiety.  What you have to remember about generalized force fields (CGenFF, GAFF, 
etc) is that transferability comes at the expense of accuracy.


What kind of unnatural residue(s) do you have?  Can it be parametrized by 
analogy from existing functional groups without going to CGenFF?  I would 
recommend relying on the protein force field as much as possible.  If you have 
to derive anything via CGenFF, absolutely run the gamut of normal parameter 
validation before relying on the parameters for production simulations.


-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] adding polyatomic species in water

[Justin Lemkul]

On 2/4/15 5:10 AM, #SUKRITI GUPTA# wrote:

Dear Gromacs Users,


I am trying to simulate a cell containing different polyatomic species like 
sulphate, glucose, acetic acid etc. in water. I start my simulation by taking 
pdb file containing 1 sulphate ion and then add remaining sulphate ions and 
other species using -cs and -ci from genbox. I use genbox command multiple time 
till all the species are added and system is solvated in water. But when I 
perform energy minimisation, the initial system starts with a very high energy 
i.e. around 10^6 range and the either it doesn't get converged or i get msg 
Segmentation fault (core dumped).


I also tried using genconf but still i was getting the same problem.


Can anyone please let me know what is wrong with my system and how can i 
correctly add all the species in my system.



Your approach for building the system is correct.  mdrun will print the atom on 
which the maximum force acts, so that should be your first point of inspection. 
 The failures you're describing indicate either unresolvable atomic clashes 
(maybe try a new value of -vdwd when building the system) or bad topology.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] chiara_marcolin wants to share a link | Gromacs

[ros...@kth.se]

chiara_marcolin wants to a share a link on the Gromacs wiki: 
http://www.gromacs.org/

chiara_marcolin says:
Goodmorning,
 I am trying to run Protein Martini tutorial using Ubuntu 14.04 and Gromacs 
software.

When I run this command: "python martinize.py -f 1UBQ.pdb -o system.top -x 
1UBQ-CG.pdb -dssp /usr/bin/do_dssp -ff martini22"

 I get this error message:

Traceback (most recent call last):
  File "martinize.py", line 5064, in 
main(options)
  File "martinize.py", line 4744, in main
ss += chain.dss(method, executable)
  File "martinize.py", line 3636, in dss
self.set_ss(ssDetermination[method](self,atomlist,executable),source=method)
  File "martinize.py", line 882, in call_dssp
if atom[0][0]!='H' and atom[0][:2]!='O2': p.stdin.write(pdbOut(atom))
IOError: [Errno 32] Broken pipe

 and I do not know how to fix it.

Could anyone help me please?
Thanks in advance
---
This email was sent at the request of a user - please do not respond to this 
email.

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[gmx-users] adding polyatomic species in water

[#SUKRITI GUPTA#]

Dear Gromacs Users,


I am trying to simulate a cell containing different polyatomic species like 
sulphate, glucose, acetic acid etc. in water. I start my simulation by taking 
pdb file containing 1 sulphate ion and then add remaining sulphate ions and 
other species using -cs and -ci from genbox. I use genbox command multiple time 
till all the species are added and system is solvated in water. But when I 
perform energy minimisation, the initial system starts with a very high energy 
i.e. around 10^6 range and the either it doesn't get converged or i get msg 
Segmentation fault (core dumped).


I also tried using genconf but still i was getting the same problem.


Can anyone please let me know what is wrong with my system and how can i 
correctly add all the species in my system.


Regards

Sukriti


[https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif]

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | 
Web:erian.ntu.edu.sg


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