from:"lloyd riggs"

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 106

2016-01-25 Thread lloyd riggs


Dear Sabuj,

 

It would be difficult to help without more info (size of system, contents of system, .mdp file, etc...).  I have not used simulated annealing in years, and when I used the software in the past, it was mostly structure determination from unknown phases (cooling an unknown partial structure from say 450 to 290 and running molreplacement every 10 degrees with several annealed structures, or taking structures from 10 seperate runs for the same thng)...

 

If the system (yours) however is 50 degrees over/under or fluctuating this much, it would indicate your equilibrium was not long enough, probably between temperature changes.  You could try increasing time segments to 5-20 ns between temperature changes, or run a simple eq, then extended sims for 10-50 ns as seperate runs at a set temperature.  As I assume a gaussian distribution, you might have to do multiple runs in either experimental set up, say 3-4 at each temperature, to generate the data with the natural gaussian distribution for kinetics (viscosity, density, etc...).

 

Good luck,

 

Stephan Watkins, PhD

 
 

Message: 6
Date: Mon, 25 Jan 2016 18:38:34 +
From: Mark Abraham 
To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Temperature Annealing
Message-ID:

Re: [gmx-users] conserved energy

2015-05-22 Thread lloyd riggs

You should also understand energy at the atomic level, the standard atom-atom inteeractions from general O chem, or chem suck as leonard jones and coulumb...per the standard, non-indexed outputs...they do not follow newtonian based energy systems even though the algorithm is newtonian based in most aspects, which I personally find a miss statement, but was shown to me years ago as true because it essentially treats everything as a moving billiard, then adds the other factors aftwerwards through intigration at set points...using tables which again I am amazed work as they are essentially from the CRC chem book, or standard books prior to computers and very small as far as input overall...pardon my spelling...and redundancy...

also for anyone with a pesudonym from Oregon state university...not pertaining to myself...as I post here, mit dieses email nicht zu oft...

Stephan Watkins, PhD

Gesendet:Freitag, 22. Mai 2015 um 22:19 Uhr
Von:Justin Lemkul jalem...@vt.edu
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] conserved energy

On 5/22/15 11:56 AM, Ahmet Yldrm wrote:
Dear users,

The total energy obtained from the .edr file is the sum of potential and
kinetic energy of system. But there is not any information about conserved
energy in manual. Maybe I couldnt find it.
I am looking for answers of the following questions:
-Which energy contributions/terms does the conserved energy include?
-How I get individual contributions (like constrains contribution) to the
conserved energy?

http://lmgtfy.com/?q=gromacs+%22conserved+energy%22+site%3Amailman-1.sys.kth.se

-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

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

2015-04-23 Thread lloyd riggs


Its seems to have changed from the versions I remember in the 5 (or maybe I remember wrong), I found you now have to use a - vector...geometry direction, I vaguely remember you could just use a - pull rate in the past...but then you can now use a single group and an absolute reference point...or different groups with multiple rates from origins or each other...had to figure that out again a week or three back...more legoish?



Steve



Gesendet:Donnerstag, 23. April 2015 um 06:30 Uhr
Von:mahender singh pharmbioc...@live.com
An:gromacs user_list gromacs.org_gmx-users@maillist.sys.kth.se
Betreff:Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Thank you dear Justin and Christopher Neale for your help.

Solute is at -z relative to the bilayer and wants to pull toward +z from the bulk water on the -Z to the +z bulk water through the membrane.
I observed that the + and the - sign in the pull_coord1_rate is associated with increase or decrease in the COM distance between the pull group and the reference group, respectively.
I am trying to split simulation into two parts i.e. each leaflet as separate SMD simulation.
When solute is moving from the -z to the center of the bilayer, it will stop here as pull_coord1_rate = -0.0020 (decrease in the COM, pull force will be - in sign, am I right that sign in force values is negative because decrease in the distance between COM of two group with time is happening), still in the last frame, COM of the molecule will not moves to the +z side and I am not able to do the second part of the simulation by setting pull_start=yes , as if I will change the pull_coord1_rate = 0.0020 it will pull it back in the -z direction (pull force will be in positive sign) (pull_geometry= distance).

@Christopher Neale
I will try the following setting and will let you know the results.

@ Justin
When I am pulling the molecule from the center of bilayer to the bulk water and the same molecule from the bulk water to the center of bilayer (by changing the sign in the pull_coord1_rate = -/+0.0020 ). pull-force v/s time graphs are looking like following (first graph is the pulling of molecule from water to the center of bilayer and second graph is from the center of bilayer to the bulk water). My query was the - and the + sign of the pull force, which I think is due to the increase and decrease in the COM distance between the pull group and the reference group, am I right?



with regards
Mahender singh


 Dear Justin:

 I think you are correct. It may not even really be that much of a hassle though one may need to be very careful in system setup for umbrellas near the center of the bilayer when using pull_start=yes rather than pull_coord1_init (i.e., one may need to make sure that the solute COM is on the side of the bilayer that one specifies with pull_coord1_vec, though having not used it myself perhaps this is not even an issue?). Separately, I presume that pull_coord1_init=0 should be identical with pull_coord1_vec = 0 0 1 or pull_coord1_vec = 0 0 -1, though if I was using the new code that would be something I would check at the outset.

 Dear Mahender:

 Based on Justins suggestion and your initial mdp file, you should try something like the following. Im still using gromacs 4.6.7 so I can not verify the accuracy of your other parameters (or even be entirely sure about these ones, but they are worth a try).

 ;; Presuming that you start with the solute at +z relative to the bilayer and want to pull toward -z
 pull = umbrella
 pull_geometry = direction
 pull_dim = N N Y
 pull_coord1_vec = 0 0 1
 pull_coord1_rate = -0.002
 pull_start = yes

 ;; I presume that
 ;; pull_coord1_vec = 0 0 1 and pull_coord1_rate = -0.002
 ;; is identical to
 ;; pull_coord1_vec = 0 0 -1 and pull_coord1_rate = 0.002

 ;; I am not sure if pull_dim = N N Y is necessary, but I dont see how it could hurt.
 ;; Presumably the distance and the vector on which the pull_coord1_rate acts are already going to be entirely along z due to pull_coord1_vec , but Id test that too if not using pull_dim = N N Y

 Please report back whether this works or whether you get strange behaviour when you hit the bilayer center.

 
 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: 22 April 2015 08:12
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

 On 4/21/15 6:54 AM, Christopher Neale wrote:
  Dear Mahender:
 
  Its a real pity that the pull_geometry = position has been removed. So now its impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.org/issues/1346 ), though no reason is given. Id suggest that you revert to a more functional version of gromacs ;)

Re: [gmx-users] calculating free energy

2015-04-20 Thread lloyd riggs



In general a realistic unfolded system would have to start at several random points in state A, and allowing it to fold into state B. This accounts for gaussian distributions of random states...


these tend to be long as the folding process is between 200 (for short) to 5-6 usecounds for longer proteins...



Some tricks...



1) starting from a half folded state, however this will not give your entire energy system from A to B

2) setting up the system with a chaperone protein (structures are in the PDB)...this gives a more rapid, but biological vs. in solvent state...

3) Reducing your system size, as unfolded proteins take up more volumn in a unit cell, thus every 20-40 nanoseconds, stop, reduce the unit cell volumn, then continue, which allows the larger scale simulations to be achieved much faster



The bar method works great for smaller molecules, but not proteins, as it if you read the paper is based on constants derived from a few hundred real kinetic determined states for small molecules. These are not a linear curve for proteins, and are usually protein specific, or even larger molecule specific if you go higher than 100 atoms...



Dont know what your doing though...



Sincerely,



Stephan L. Watkins, PhD


Gesendet:Sonntag, 19. April 2015 um 03:41 Uhr
Von:Christopher Neale chris.ne...@alum.utoronto.ca
An:gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se, gmx-us...@gromacs.org gmx-us...@gromacs.org
Betreff:Re: [gmx-users] calculating free energy

How about temperature replica exchange with de novo folding, then convert the probabilities of the folded and unfolded states into a free energy difference? Youll obviously need to be really careful about cutting off a sufficient amount of initial simulation time as equilibration, but you might be able to get a good idea of how much to cut if you repeated it once from unfolded and once from folded.

Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of nazli kashani javid nazlikja...@gmail.com
Sent: 18 April 2015 11:24
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] calculating free energy

Hi all,

I know there are some methods for calculating free energy of* binding*
between a ligand and a receptor.

1.Are there any methods for calculating free energy of *unfolding *proteins?

4_helix bundle protein makes my system,

2.Is scientifically reasonable for my system to calculate free energy in
the same way as described in tutorial number 6, methane in water ( coupling
parameter : vdw interaction)?

Thank you

any help is appreciated.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.



-- 
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.

Re: [gmx-users] trjconv_d errors

2015-04-07 Thread lloyd riggs

Thats what I thought.

I recieved no response, but can jimmy rigg the entire thing to be processed on 4.6.7 from a 5.0.1 run, however it looses the temperature?

Sincerely,

STephan L. Watkins, PhD

Gesendet:Montag, 06. April 2015 um 02:51 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] trjconv_d errors

Dear All,

I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install.

Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files. I was simply interested mostly as my secound problem is, if I include anything other than the standard energy groups of protein non_protein (say x y z), the performance goes from 20 ns a day for my system, to 10 ns a day. Thus I was going to rerun everything after the grid usage with -rerun and a changed energy group list just to make my life easier.

I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f in.trr -o out.trr or out.xtc works fine. It will even process a standard 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I get a version error.

Is this a) a bug and b) a if so or not, does someone have a work around?

I have also tried gmx_d trjconv, and I searched the mail archives, and the only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema, stating if the files were larger than a few gigs, there was a memory error. I origionally thought this the error, however decided to run test first with small 100MB-2 G runs to test it, and this was not the problem.

Sincerely,

Stephan L. Watkins, PhD

-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant 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.

--
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.

Re: [gmx-users] trjconv_d errors

2015-04-05 Thread lloyd riggs

Dear All,

I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install.

Is this a) a bug and b) a if so or not, does someone have a work around?

Sincerely,

Stephan L. Watkins, PhD

--
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.

Re: [gmx-users] Axis

2014-11-04 Thread lloyd riggs


Dear Gromacs users,



Is there a way to change the x y z axis as read by the software, in just the simple pdb/gro file? I want to transpose the z onto x as read by the computer.



Stephan Watkins

-- 
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.

Re: [gmx-users] Version 12

2014-10-31 Thread lloyd riggs


Im getting a Attempting to read a checkpoint file of version 15 with code of version 12, does anyone know off hand which is version 12 ? Im guessing lik 4.5.6 , but dont know.



Stephan Watkins

-- 
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.

Re: [gmx-users] Membrane simulations

2014-10-20 Thread lloyd riggs


Dear All,



So I have been doing membrane simulations on a small (really small) node for a few months, and was able to get in a few hundred nanoseconds of time. I now have added 4 inositol lipids, and repeatedly encounter some errors as follows.



I set the time in the eq for 0.0005 and it runs about 25000 steps. I then move up to a normal sim at 0.002 and it runs about 25000 steps then crashes with a particle moved to far error. On inspection, these vary each time, but are always a membrane lipid /cholesterol or inositol atom, usually trying to move ithrough a periodic boundary temporarily? I then run the sim again (continuation) for 25000 steps at 0.0005 again then it crashes again with the same eror. I then Switch back to 0.002 as a continuation, and the same. I have done this for around 10 ns now? I woundered if there were any suggestions, as it makes it impossible to run a simulation unless you baby sit it constantly, and precludes submitting it to a server? Please excusse my spelling.



Stephan Watkins, PhD





-- 
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.

Re: [gmx-users] MD workstation

2014-10-16 Thread lloyd riggs



Is there any progress in openCL versions of Gromacs, as it is listed on the developer site? Just askin. One thing I ran across is one can get integrated GPU arrays on a board if you find say Russian board designs from China for about the same price with 10x the computational speed, but the boards would be largly OpenCL dependent.



Stephan Watkins


Gesendet:Donnerstag, 16. Oktober 2014 um 20:21 Uhr
Von:Szilrd Pll pall.szil...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:Re: [gmx-users] MD workstation

On Thu, Oct 16, 2014 at 3:35 PM, Hadhzi dm hada...@gmail.com wrote:
 May I ask why your config is better than e.g.

 2x Intel Xeon E5-2620 CPUs (2x405)
 4x GTX 970(4x 330)
 1x Z9PE-D8 WS (449)
 64 GB DDR3 (600)
 PSU 1600W, (250)
 standard 2TB 5400rpm drive, (85)
 total: (~3500)

Mircos suggested setup will give much higher *aggregate* simulation
throughput. GROMACS uses both CPUs and GPUs and requires a balanced
resource mix to run efficiently (less so if you dont use PME). The
E5-2620 is rather slow and it will be a good match for a single GTX
970, perhaps even a 980, but it will be the limiting factor with two
GPUs per socket.

 As for your setup...can I use that 4 nodes in parallel for 1 long
 simulation or 1 FEP job?

Not without a fast network.

 What are the weak points of my workstation?

The CPU. Desktop IVB-E or HSW-E (e.g. i7 49XX, 59XX) will give much
better performance per buck.

Also note:
* your smaller 25k MD setup will not scale across multiple GPUs;
* in FEP runs you, by sharing a GPU between multiple runs you can
increase the aggregate throughput by quite a lot!

Cheers,
--
Szilrd

 Best,
 Adam


 2014-10-16 23:00 GMT+10:00 Mirco Wahab mirco.wa...@chemie.tu-freiberg.de:

 On 16.10.2014 14:38, Hadhzi dm wrote:

 Dear GMX Stuff and Users,
 I am planning to buy a new MD workstation with 4 GPU (GTX 780 or 970)
 or 3
 GPU (GTX 980) for 4000.
 Could you recommend me a setup for this machine?
 1 or 2 CPU is necessary? 32/64 GB memory? Cooling? Power?


 - What system (size, type, natoms) do you plan to simulate?

 - Do you have to run *only one single simulation* over long time
 or *some similar simulations* with similar parameters?


 The systems are kind of mix:
 MD:
 smallest system: 25k atoms, spc/tip3p, 2fs/4fs, NPT, simulation time:
 500-1000ns
 biggest system: 150k atoms, spc/tip3p, 2fs/4fs, NPT, simulation time:
 100-1000ns
 FEP (free energy perturbation): ligand functional group mutation
 25k-150k atoms, in complex and in water simulations, production
 simulation:
 5ns for each lambda window (number of windows: 12)


 In this situation, Id probably use 4 machines for 1000 each,
 putting in each:
 - consumer i7/4790(K), 300
 - any 8GB DDR3, 75-80
 - standard Z97 board, 100
 - standard PSU 450W, 40
 - standard 2TB 5400rpm drive, 85

 the rest of the money (4 x 395), Id use for 4 graphics
 cards, probably 3 GTX-970 (330) and one GTX-980 (550) -
 depending on availability, the actual prices, and
 your detailed budget.

 YMMV,


 Regards

 M.

 --
 Gromacs Users mailing list

 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/GMX-Users_List before posting!

 * Cant 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.

 --
 Gromacs Users mailing list

 * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

 * Cant 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.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.



-- 
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.

Re: [gmx-users] protein-ligand complex by gromacs

2014-09-09 Thread lloyd riggs

did you center everything, or are you just looking at it in VMD?


Gesendet:Montag, 08. September 2014 um 18:30 Uhr
Von:Mahboobeh Eslami mahboobeh.esl...@yahoo.com
An:gmx-us...@gromacs.org gmx-us...@gromacs.org
Betreff:[gmx-users] protein-ligand complex by gromacs

hi GMX users


i have simulated the protein-ligand complex by gromacs. Ive repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box.
Ive checked all of the input files and the steps , but I did not understand why this happened.
Please help me .
Thank you for your kindness
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.



-- 
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.

Re: [gmx-users] g_mindist for hydrophobic interactions

2014-09-09 Thread lloyd riggs

you should go down the list and use all the tools, and use some from seperate software. In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian distribution, but it removes these. Somone e.lse here probably has better contributions though. It is hard to say without seeing the raw data though.

Stephan Watkins

Gesendet:Montag, 08. September 2014 um 10:25 Uhr
Von:Ca C. devi...@hotmail.com
An:gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se
Betreff:[gmx-users] g_mindist for hydrophobic interactions

Dear All,
I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptors transactivation.
Is g_mindist a good tool for this purpose? Do you have more suggestions?
Moreover, should I use trjconv for pbc treatment before running g_mindist?

Thank you in advance

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] centering with trjconv

2014-08-27 Thread lloyd riggs

I like the fit progressive sometimes more...

Stephan

Gesendet:Dienstag, 26. August 2014 um 21:49 Uhr
Von:Tsjerk Wassenaar tsje...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:Re: [gmx-users] centering with trjconv

Hey :)

What about -pbc nojump -center ?

Cheers,

Tsjerk

On Tue, Aug 26, 2014 at 8:12 PM, Justin Lemkul jalem...@vt.edu wrote:

On 8/26/14, 12:30 PM, Eric Smoll wrote:

Hello GROMACS users,

I have created an infinite liquid film system by building a slab of
molecules in a 3D periodic unit cell where two dimensions of the film (x
and y) extend out to the edge of the unit cell and one (z) does not.

I found the slab drifts along the z-dimension during MD and I am trying to
post-process the trajectories to anchor the slab in the center of the unit
cell.

trjconv -pbc mol -center -boxcenter works well for most trajectories
*unless* the slab drifts so much that it comes in contact with the z
boundary. When this occurs, trjconv -pbc mol -center -boxcenter anchors
it in a different location. Any ideas how I can anchor the system to the
center of the unit cell in this situation?

The -fit options should help here, either progressive or translation.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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!

* Cant 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.

--
Tsjerk A. Wassenaar, Ph.D.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

[gmx-users] Membrane simulations

2014-08-13 Thread lloyd riggs


Dear GMX users,



I ran across a nice web page, I believe from a brazilian group, for generating membranes of any compnents (pdb). This was months ago, and after a few days of trying, I cannot find the page again. It was capable of makeing bilayers, as well as other shapes, including small micelles. I have already looked at http://www.cellmicrocosmos.org/index.php/download/downloadcm2 , and all relavant gromacs tutorials, as well as links to find them...so any help is appricaited. They have nice readable source code, and the scripts were simple and freeware.



Sincerly,



Stephan Watkins, PhD

OSU botany department





-- 
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.

Re: [gmx-users] Membrane simulations

2014-08-13 Thread lloyd riggs

Thank you very much. Yes I did.

Stephan

Gesendet:Mittwoch, 13. August 2014 um 23:09 Uhr
Von:Victor Rosas Garcia rosas.vic...@gmail.com
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] Membrane simulations

Hello Stephan,

Do you mean PACKMOL?

http://www.ime.unicamp.br/~martinez/packmol/

VIctor

2014-08-13 0:58 GMT-05:00 lloyd riggs lloyd.ri...@gmx.ch:
Dear GMX users,

I ran across a nice web page, I believe from a brazilian group, for
generating membranes of any compnents (pdb). This was months ago, and after
a few days of trying, I cannot find the page again. It was capable of
makeing bilayers, as well as other shapes, including small micelles. I
have already looked at
http://www.cellmicrocosmos.org/index.php/download/downloadcm2 , and all
relavant gromacs tutorials, as well as links to find them...so any help is
appricaited. They have nice readable source code, and the scripts were
simple and freeware.

Sincerly,

Stephan Watkins, PhD
OSU botany department

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

2014-06-07 Thread lloyd riggs

Its probably a single atom name typo unless its the end residue ( I know from experience after 45 minuts or more, typos become extreemly difficult to spot for pshchological reasons), but you would need to show the in file (pdb) and probably the top for a spot check.

Stephan

Gesendet:Samstag, 07. Juni 2014 um 16:32 Uhr
Von:Vedat Durmaz dur...@zib.de
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:[gmx-users] specbond identified by pdb2gmx but not added to topology

dear gmx users/team,

ive defined some simple residues (5 monomeric units) in aminoacids.rtp,
residues.dat and aminoacids.hdb that i want to use for the modelling of
small polymers. the polymer may be highly bifurcated due to a branching
T piece among the monomer units.

all possible intermolecular connections (about 20) between the units are
defined in the specbonds file according to the following pattern:

...
XYB CG2 1 XYX O 1 0.16 XYB XYX
...

there is no need for new atom types or changes in ffbonded/ffnonbonded
since all atoms and the resulting bonds also occur in typical amino
acids. however, when starting pdb2gmx

pdb2gmx -ff amber99sb -f input.pdb -o polymer.pdb -p polymer.top -ignh
-water none

with 12 residues/units (and several bifurcations) requiring 11
additional intermolecular bonds to be read from the specbond file, i get
a nice resulting topology containing all desired bonds except for one
lone 0.143nm bond between atom CG2 (amber type CT) of residue 3 (XYB)
and atom O (amber type OS) of residue 7 (XYX). curiously, this missing
bond is listed in the distance matrix output of pdb2gmxt related to
specbond:

...
29 out of 29 lines of specbond.dat converted successfully
Special Atom Distance matrix:

XYL1 XYX2 XYX2 XYX2 XYB3 XYB3 XYB3
CG25 O6 OG19 CG210 O11 OG114 CG215
...
XYX7 O31 0.714 0.635 0.487 0.293 0.483 0.303
-0.143- here it is
...
...

but when it comes to the linking stage a little further in the output,
this bond is neglected whereas the other ten bonds are set as desired:

...
Linking XYL-1 CG2-5 and XYX-2 O-6...
Linking XYX-2 OG1-9 and XYX-4 CG2-20...
Linking XYX-2 CG2-10 and XYB-3 OG1-14...
Linking XYX-4 O-16 and XYL-5 CG2-25...
Linking XYX-4 OG1-19 and XYL-6 CG2-30...
Linking XYX-7 OG1-34 and XYX-8 CG2-40...
Linking XYX-7 CG2-35 and XYR-12 O-56...
Linking XYX-8 O-36 and XYL-9 CG2-45...
Linking XYX-8 OG1-39 and XYB-10 CG2-50...
Linking XYB-10 OG1-49 and XYL-11 CG2-55...
...

does anyone have some hint or an idea of what might be suppressing the
linking of that bond? ive tried it with gromacs 4.5 as well as 4.6
without any difference in the output.

thanks in advance and a good weekend,

vedat

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] Need some help with membrane simulation

2014-06-06 Thread lloyd riggs


Has anyone done an all atom 53a6 or 54a7 .itp/rtp that can be downloaded (reguarding protein/amono acids or and nucleic? I can make one in a week (for proteins) just using a topology builder and modifying things, there are already lipids around 100 with all atom in either field, but after reviewing liturature, even the hybrid 53a6 is better than opls or charm all atom as far as fitting computational against real measured biochem. I assume if one did this, it would have to be tested first, or in parallel to any work, however I have found multiple relics and hints of people whom obviously already did this, but can not find an .itp or .rtp for this? this is also in reguards to membrane simulations, as most of the comparisons I have seen show even berger hybrid UA/charged hydrogens in 53a6 as much (by about 1-5% difference) vs around 10-20% difference in biochem Vs comp. for all other force fields.



Sincerely,



Stephan Watkins



Gesendet:Donnerstag, 05. Juni 2014 um 23:31 Uhr
Von:Piggot T. t.pig...@soton.ac.uk
An:gmx-us...@gromacs.org gmx-us...@gromacs.org
Betreff:Re: [gmx-users] Need some help with membrane simulation

I havent tried it at all, but in the release notes for 5.0.x there is a LJ force switching option mentioned. This would probably be preferable for membrane simulations using CHARMM36, rather than switching the potential.

Cheers

Tom

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: 05 June 2014 22:12
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Need some help with membrane simulation

On 6/5/14, 4:57 PM, Ali Khan wrote:
 Justin,

 4.6.5 does not have Potential-switch-Verlet. When I added the other
 changes, I still had the same error.


Likely something more fundamental is wrong with the system. What was the
outcome of EM? Exact numbers produced by mdrun, please.

 Are these recommendations ones that I should generally use when
 implementing charmm in gromacs?

Yes. Im still experimenting with all the new Gromacs features, but as best I
can tell, in terms of reproducing a normal CHARMM setup:

cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = Potential-switch
coulombtype = PME
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2

-Justin



 On Thu, Jun 5, 2014 at 4:29 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/5/14, 2:47 PM, Ali Khan wrote:

 I am using the charmm36 force field.

 *My energy minimization .mdp file:*

 ; minim.mdp - used as input into grompp to generate em.tpr
 ; Parameters describing what to do, when to stop and what to save
 integrator = steep ; Algorithm (steep = steepest descent minimization)
 emtol = 1000.0 ; Stop minimization when the maximum force  1000.0
 kJ/mol/nm
 emstep = 0.01 ; Energy step size
 nsteps = 5000 ; Maximum number of (minimization) steps to perform

 ; Parameters describing how to find the neighbors of each atom and how to
 calculate the interactions
 nstlist = 1 ; Frequency to update the neighbor list and long range forces
 ns_type = grid ; Method to determine neighbor list (simple, grid)
 rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
 coulombtype = PME ; Treatment of long range electrostatic interactions
 rcoulomb = 1.2 ; Short-range electrostatic cut-off
 rvdw = 1.2 ; Short-range Van der Waals cut-off
 pbc = xyz ; Periodic Boundary Conditions (yes/no)
 vdw-type = cutoff
 vdw-modifier = Potential-shift-Verlet
 cutoff-scheme = Verlet





 *Temperature equilibration .mdp file:*

 title = NVT equilibration
 define = -DPOSRES ; position restrain the protein
 ; Run parameters
 integrator = md ; leap-frog integrator
 nsteps = 50 ; 2 * 50 = 1000 ps
 dt = 0.002 ; 2 fs
 ; Output control
 nstxout = 0
 nstvout = 0
 nstenergy = 500
 nstlog = 0
 ; Bond parameters
 continuation = no ; first dynamics run
 constraint_algorithm = lincs ; holonomic constraints
 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
 lincs_iter = 1 ; accuracy of LINCS
 lincs_order = 4 ; also related to accuracy
 ; Neighborsearching
 ns_type = grid ; search neighboring grid cells
 nstlist = 5 ; 10 fs
 rlist = 1.2 ; short-range neighborlist cutoff (in nm)
 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
 rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
 rcoulomb-switch = 0
 rvdw-switch = 0.8


 Use rvdw-switch = 1.0.


 ; long-range cut-off for switched potentials
 rlistlong = 1.4


 Probably never had the desired effect in terms of using CHARMM force
 fields and isnt necessary. The Verlet scheme with rlist = 1.2 should
 provide adequate buffer space.


 ; Electrostatics
 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
 pme_order = 4 ; cubic interpolation
 fourierspacing = 0.16 ; grid spacing for FFT
 ; Relative dielectric constant for the medium and the reaction field
 epsilon_r = 1
 epsilon_rf = 1
 ; Temperature coupling

Re: [gmx-users] New Molecule Topology

2014-05-30 Thread lloyd riggs

I think the Ausi ATB is a bit beter for initial topologies,but still needs some input afterwards. They usually have less to change around needed, or beter charge sets, but tend to have problems with adding a hydrogen. Only for 53a6 though. Also, just loking at the ff topoloy you canput one together from scratch from what is already in gromacs, but painfull...there are a large amunt of MDs with all atom or berger lipids in a 53a6 which should work with a7 as well, and the ATB has a few constructed all or UA lipids, cholestorols on its site already done...

My opinion,

Stephan Watkins

Gesendet:Donnerstag, 29. Mai 2014 um 16:55 Uhr
Von:Todor Antonijevic t_ant...@uncg.edu
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] New Molecule Topology

Hi Justin,

Thank you for you answer.
It sounds to me that using PRODRG server for the initial topology and then
correcting atom types and other parameters according to Berger lipids is
acceptable method.

What about constructing cholesteryl oleate molecule by gluing together
known cholesterol force field with oleate chain taken from POPC?

Thank you in advance,

Anton

On Wed, May 28, 2014 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote:

On 5/28/14, 1:33 PM, Todor Antonijevic wrote:

Hi,

I would like to create a topology file for cholesteryl oleate molecule.
Is it a good practice to use PRODRG server to generate all connections,
and
then to change atom types and parameters according to the Berger force
field?

Is there a better approach?

No matter how you produce the initial topology (PRODRG, ATB, etc), youll
likely end up gutting nearly the entire topology to replace the atom types,
charges, and bonded parameters.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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!

* Cant 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.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] (no subject)

2014-05-25 Thread lloyd riggs



I have an interesting question reguarding NH2 attached to cyclic rings in topology files. I have seen them represented in a somewhat SP3 state, where the hydrogens are held as if there were almost 3, rather than two. I have also seen them artificially flatened with an improper dihedral, which allows them to rotate around the N-C bond. My question is which is correct, and if they are given an improper dihedral how would this effect the energy calculations. These do commonly occure such as nucletides, but mostly I refer to small molecules with gnerated topologies. I have looked up in chem liturature and found in empirical studies they do indeed remain flatened in reguard to the plane of the ring, rotating around the bond, however in chemistry text and papers treeting them in reactions, etc, they are in an SP3 state?



Stephan Watkins


-- 
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.

Re: [gmx-users] binding sites with MD

2014-05-25 Thread lloyd riggs

Theres one paper that shows (VMD film) and talks about diffusion times I know of, however I do not know of any simply looking for ligands via setting up an MD system, then running them long enough to see if they find a site, this seems like a large amount of excessive work as the systems are much more complicated, and require much more computer power. Usually the rule of thumb in the process is to first do massive amounts of docking, and then move to MD to validate suspected sites. This may be a preference as several strategies are published approaching this.

Stephan Watkins

Gesendet:Samstag, 24. Mai 2014 um 12:24 Uhr
Von:Nidhi Katyal nidhikatyal1...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:[gmx-users] binding sites with MD

Hi all,

I would like to ask if unbiased MD in nanoseconds time scale be used to
find the potential binding sites of ligand with protein?

I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with
random placement of ligand initially. In the time interval between 40 to
50ns, movement of ligand molecules can be seen around certain sites only
for both the runs. Can these sites be considered as binding sites? Also,
ligand molecules are involved in both hydrophobic and hydrogen bonding
interactions with these sites.

Thanks in advance.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] entropy vs time plot

2014-05-21 Thread lloyd riggs


Yah but youll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas).



Stephan Watkins



Gesendet:Mittwoch, 21. Mai 2014 um 06:54 Uhr
Von:tarak karmakar tarak20...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:Re: [gmx-users] entropy vs time plot

Hi Tsjerk,
Thanks for the quick reply.
I did the following

g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v
eigenvec.trr -av average.pdb -b 0 -e 1
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 1

What I want to plot is similar to this.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/

Is there any flag for this?
Ive checked g_covar -h and g_anaeig -h but didnt get the proper way.

Thanks,
Tarak



On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi Tarak,

 You will have to use -b/-e to set the start and end times.

 Cheers,

 Tsjerk


 On Tue, May 20, 2014 at 12:18 PM, tarak karmakar tarak20...@gmail.com
 wrote:

  Dear All,
  Could anyone tell me how to plot configurational entropy as a function of
  simulation time?
  Do I need to manually specify the -dt(say after each 1 ns) during the
  g_covar and then do g_anaeig in each of the step?
 
  thanks,
  Tarak
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Cant 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.
 



 --
 Tsjerk A. Wassenaar, Ph.D.
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

 * Cant 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.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.



-- 
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.

Re: [gmx-users] GPU in Ubuntu

2014-05-12 Thread lloyd riggs

From my experience its fine, the main problems are annoying changes to gedit, other side software and a few bugs that pop up, as the come out with a new release rather quickly...I usually avoid the new releases for at least 6 months now, and havnt really had much problem with larger bugs, such as missing or incompatable libraries since...except for say their last changes in searching files, etc...smaller bugs or anoying changes.

Steve

Gesendet:Samstag, 10. Mai 2014 um 22:40 Uhr
Von:Albert mailmd2...@gmail.com
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] GPU in Ubuntu

it is better to choose a stable Linux for computational work. I
recommend the following:

Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise

Ubuntu is on not stable enough for professional work according to my own
experiences.

On 05/10/2014 10:06 PM, lloyd riggs wrote:
Dear All,
I recently ran into a problem with a small geforce 610, and aside from
woundering if it was worth the effort, found in Ubuntu 13.10 gromacs
can not find the GPU. The Nvidia site found this problem and states
to install libcudart.5.5.so or higher, i tried this and the 6.0 as
well, with no luck.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] GPU in Ubuntu

2014-05-10 Thread lloyd riggs



Dear All,



I recently ran into a problem with a small geforce 610, and aside from woundering if it was worth the effort, found in Ubuntu 13.10 gromacs can not find the GPU. The Nvidia site found this problem and states to install libcudart.5.5.so or higher, i tried this and the 6.0 as well, with no luck. The OS itself also has a hard time finding the GPU, however it is found with any comand line tool rather easy as a PCI device. Any fixes, thoughts or suggestions as this is simply for set up for systems (EM, initial system setup).



A secound question, does anyone know of server based gromacs, as I am at the moment hitting a wall with the universities resources (lack of access for wierd reasons) and wanted to persue simulations of a few things. I am aware of Groningens site, but have not found much for gromacs any place else, although there are several others with different formating, resulting in users are only able to use their (the sites) online analytical tools which are usually very limited in scope? With the Groningen site, the only complaint is there is no fine tuning of varied parmeters, which means the submission works or does not (ie no setting of mdrun parameters such as -rcon, -dd, -mpi , only a .tpr and or pdb file are submitted to the system) It is better than nothing, but just a critique, as it worked for me for standard systems, but crashed for me with wierd ligands when I used it breifly.



Sincerely,



Stephan Watkins, PhD




-- 
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.

Re: [gmx-users] PEG residue

2014-03-18 Thread lloyd riggs

You can get most of these tabulated in a CRC book, an older one is easier to read (circa 1988), online through the international union of physics and chemsitry web site(s), or look over the partial force field (54a7) and locate the same bonds/angles such as aminos and nucleic acids, as the sugar/ring other things will have roughly all the info with just different naming schemes for atoms/residues...

Stephan Watkins

Gesendet:Dienstag, 18. Mrz 2014 um 00:05 Uhr
Von:dan42 dan...@comcast.net
An:gmx-us...@gromacs.org
Betreff:[gmx-users] PEG residue

I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG
(O-C-C)n with only H on one terminal and OH on the other. I know that I need
to add a residue entry to the forcefield for example to aminoacids.rtp in
the gromos54a7.ff folder. However, I do not know how to construct the
residue entry. I do know the format but I do not know what values to enter
for bonds, angles, dihedrals ect. Can anyone help me?

--
View this message in context: http://gromacs.5086.x6.nabble.com/PEG-residue-tp5015237.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] binding delta G, H and S for ion-protein

2014-03-17 Thread lloyd riggs

Dear Board,

I have done this with a steered MD, using covarience, etc...in the end there are nice delG and H,S line graphs...the only argument I have heard however is when doing the subtraction the third curve always gives the correct repective energy change, but the delG line graph may not always represent the energy path correctly as there becomes a large amount of overlap in energy changes between other groups not in the index grp used (ions, h2o, long range effects lowering conformational states such as a 3 water bridge to another protein) ...only making it much more cumbersome, or making the delS or H have much higher STDV or total error that can for a biochemist looking at say a small ligand binding energy squirm (delG say of 20 kCal/mol but STDV or error at +/- 10 kCal/mol where say a protein protein or DNA interaction may have dips and wells in the 100s of kCal/mol range so not quite as problematic...all assuming one is not using a QQMM where the errors go down one or two orders ofmagnitude)...theH/S pathways though can be informative especially for biologist looking at macromolecules...I would be interested in opinions/thoughts on these differences though...

Stephan Watkins

Gesendet:Montag, 17. Mrz 2014 um 09:26 Uhr
Von:David van der Spoel sp...@xray.bmc.uu.se
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] binding delta G, H and S for ion-protein

On 2014-03-16 19:05, Andrew Bostick wrote:
Dear Justin

Thanks for your answer.

All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating
free energy (G). In addition to free energy (G), I want to calculate
enthalpy (H) and entropy (S).

Are you sure can I use above methods for calculating both of enthalpy (H)
and entropy (S)?

You can compute H and S by doing a temperature series and use the Van t
Hoff equation. A bit expensive though. Sometimes for well-defined
systems if you do a PMF you can subtract the enthalpy coming from the
simulation to obtain the entropy. See e.g.
PNAS 108 pp. 6838-6842 (2011)

Best wishes

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] MD SIMULATIONS ON A CLUSTER

2014-01-30 Thread lloyd riggs

Yes it is, or should be from my experience. You need to look at the mailinglist, and it takes time t work out somethings as there also system (your simulation) dependent. Mostly these are parameters such as domain decomposition sizes, number of threads, -rdd, -rcon -dds and others (I found more important for speed) -mpi vs -nt and -ntomp and similar parameters, along with some -npme. The mail list has alot more, but in the end these have to be optimised based on your system, deminsions, whats in it, etc...in the end you see a speed up untill you get a good 200 atoms per unit cell in the decomposed grid is what I found, a 4-5 day simulation, 4000 amino acids and 169,000 atoms went to 12-15 hours at 4-5 ns simulation time.

Sincerely,

STephan Watkins

Gesendet:Donnerstag, 30. Januar 2014 um 19:50 Uhr
Von:MUSYOKA THOMMAS mutemibiochemis...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:[gmx-users] MD SIMULATIONS ON A CLUSTER

Dear Users,
I have been doing 10 ns MD simulations of protein-ligand complexes on a
local cluster of 64 cores using GROMACS 4.5.7. However, there seems to be
no much difference in the time it takes to complete one cycle of an mdrun
(3-days - same as when I used a machine with 4 cores).

Will be appreciative to know if its possible shorten the time period.

See the following command that I have incorporated in a python script so as
to automate the md process right from the beginning.

md=md.mdp
os.system(mdscriptcopy)
finalmdruncommand=grompp -f %s -c %s -t %s -p %s -n %s -o %s%
(md,nptgro,nvtcpt,topoltop,indexfile,mdtpr)
os.system(finalmdruncommand)
*finalrun=mdrun -v -deffnm md*
os.system(finalrun)

*Do all the good you can, By all the means you can, In all the ways you
can, In all the places you can,At all the times you can,To all the people
you can,As long as ever you can. - John Wesley. *
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] pca

2014-01-23 Thread lloyd riggs

Suggestions,

You can look at your plots from g_sham in an editor, and simply cut/past then add the matricies portion in something like qtiplot/Scidavis, or you need to back track and use covarience in the gromacs auxillary scripts (g_covar/aneig, etc...) and track down some matrix scripts to do the same thing. This later allows 2 single column PCs from your output files to be used to generate 2D plots with your dfined boundries, if you find the right ones (scripts), which are easier to manipulate than .xpm files. I found several dozen matrix manipulation scripts written in everything from C++ to perl and python...

Stephan Watkins

Gesendet:Montag, 20. Januar 2014 um 10:48 Uhr
Von:pratibha kapoor kapoorpratib...@gmail.com
An:gmx-us...@gromacs.org
Betreff:[gmx-users] pca

Dear all gmx-users

I have done pca at three different temperatures and would like to draw
combined 2D free energy landscape (pc1 versus pc2) and 3D free energy
landscape (pc1, pc2, and energy).
I have used g_sham and created three different 2D plots. My question is how
to combine these three plots in order to get all information from three
temperatures in one plot? Also please guide me in creation of 3D plots.

Thanks.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] Potential energy calculations

2013-12-27 Thread lloyd riggs

I got boared at one point and indexed everything, and was looking at total energy, but found if you look at any parameter (LJSR, etc...) for solvent they appear like sinusoidal...but was jsut in my brain equating these to potential energy, and assumed the OP was trying to look at only the DMSO not the system, thus trying to make a stab at it. Couldnt figure out how to deliniate the two, as the error estimates would overlap to the point of making either non-significant, without a perterbation, and you cant direct plot potential for an indexed molecule (summed other energies), but the potential for a whole simple system has a very large standard error and drift, which overlaps the small molecules potential energies, in any case, I let it rest now happy hollidays...

Sincerely,

Stephan Watkins

Gesendet:Samstag, 28. Dezember 2013 um 00:52 Uhr
Von:Justin Lemkul jalem...@vt.edu
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] Potential energy calculations

On 12/26/13, 4:52 PM, lloyd riggs wrote:
Yes I know what you mean, however when your looking over a unit cell and trying
to define a single molecule in the solvent (even as represented by the entire
solvent makup), does it properly alighn the energy based on the averidged zero
point. I ask, not knowing, but playing with this (single small molecules), I
found the systems standard error swamps the potential energy, and you then get a
proper shaped graph, where the axis has to be corrected by an energy term (is
what I meant by zeroing). I did this with just h2o playing around out of
boardom at some point...as I had run across something showing perfect sinusoidal
energy graphs of waters/solvent...but the trajectory used contained 5 ions and a
single proteinDMSO is a tiny molecule...

Were not dealing with a single molecule, at least assuming I understand what
the OP is discussing. One has a homogeneous box of solvent, such that the
potential energy of the system can be divided evenly between equivalent
molecules and averaged over time. The literature often reports the
configurational energy of such a liquid.

Im not entirely sure what it is that you were playing around with, but such
decompositions as these are not suited for heterogeneous systems, and what
youve come up with really just sounds like a way of looking at the
interconversion of kinetic and potential energy.

-Justin

Stephan
*Gesendet:* Donnerstag, 26. Dezember 2013 um 14:04 Uhr
*Von:* Justin Lemkul jalem...@vt.edu
*An:* gmx-us...@gromacs.org
*Betreff:* Re: [gmx-users] Potential energy calculations

On 12/26/13, 5:30 AM, lloyd riggs wrote:
Zero it-- If you plot a potential energy value strait from the simulation it
will be something like point a) -7000 point b) -7050 across a single
simulation. Thus you have to find a beginning point and subtract it across the
run. Additionally, fluctuations may dictate 10 or so runs to determine a good
mean, as the drifet or error might be 20 kcal/mol in a system. As I read your
other post, I would assume the experiment would be non random placement of DMSO
in water (say a wall system), otherwise you would be looking at a single
molecules energy dictated by conformational space over time...ie something like
Justins post...which you still may have to calculate a mean for, but I assume
this is done through the -nmol option. You still also may have to zero it,
but I am not sure, direct use of g_energy gives abitrary starting points as
above from my experience.

The values printed by g_energy are not arbitrary. They are the energy of a mole
of equivalent systems of a given configuration, hence their large magnitude.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu (410) 706-7441

==
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu (410) 706-7441

==
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Potential energy calculations

2013-12-26 Thread lloyd riggs

Yes I know what you mean, however when your looking over a unit cell and trying to define a single molecule in the solvent (even as represented by the entire solvent makup), does it properly alighn the energy based on the averidged zero point. I ask, not knowing, but playing with this (single small molecules), I found the systems standard error swamps the potential energy, and you then get a proper shaped graph, where the axis has to be corrected by an energy term (is what I meant by zeroing). I did this with just h2o playing around out of boardom at some point...as I had run across something showing perfect sinusoidal energy graphs of waters/solvent...but the trajectory used contained 5 ions and a single proteinDMSO is a tiny molecule...

Stephan

Gesendet:Donnerstag, 26. Dezember 2013 um 14:04 Uhr
Von:Justin Lemkul jalem...@vt.edu
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] Potential energy calculations

The values printed by g_energy are not arbitrary. They are the energy of a mole
of equivalent systems of a given configuration, hence their large magnitude.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu (410) 706-7441

==
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] Potential energy calculations

2013-12-23 Thread lloyd riggs

Did you zero it ?

Stephan Watkins

Gesendet:Dienstag, 24. Dezember 2013 um 01:33 Uhr
Von:virk virkbl...@yahoo.com
An:gmx-us...@gromacs.org
Betreff:[gmx-users] Potential energy calculations

Dear Users,

I am try to simulate DMSO molecules. I am getting potential energy values of

Energy Average Err.Est. RMSD Tot-Drift
---
Potential -28160.8 4 259.924 24.189
(kJ/mol)

But according to some papers average potential energy value is 49.1
(KJ/mol).

Everything else seems to match this paper (density, diffusion coefficient)
except potential energy.

Am I missing something over here or my system is wrong.

I would be very thankful for your help and time.

Amninder Virk

--
View this message in context: http://gromacs.5086.x6.nabble.com/Potential-energy-calculations-tp5013495.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] Bin files of g_sham

2013-12-18 Thread lloyd riggs

Trying to help I would say I am trying to remember some things I did some time ago. That said, your missing the time column as your first input. You are making a 2D energy plot is what your telling it to do, you can also tell it not to expect a time which would be correct for your case, however this is a landscape your generating. It is already a total energy landscape in 1 nm by 2 nm 2D volumn, what your doing is trying to use the boltzman inversion equation in the g_sham to break it down into gibbs, enth and entro as .xpm plots. Your bins are the pixels or points in the landscape I believe, thus the binwidth is the xmin and max, but I amnot 100% sure how the numbering goes. You can check it against the image file generated (look at it with gedit, the pixel portion will tell you).

One way to get it to work, would be to supply a free energy single column (or time, then single energy column), however someone might correct me on this (I hope) if I am wrong.

However your origional question was to look up or coordinate a line graph gibbs energy plot, with a frame in your trajectory. Thus I believe you want to look at a linear plot of your energy change over time. If you generated the eigen vectors already, there are methods in these techniques to look at frames versus energy (total). You can also if you designed your experiment as a pulled/steered free energy experiment, use the g_wham, with no bootstraping or autocorrelation, etc...with one trajectory, and it is a sham. Otherwise, your using the wrong things to get what you want (g_ scripts in gromacs), and need to read the manual again. You can, with an index for only what you want, extract total energy and plot it as well versus frame, which might give you what you want also...using just g_energy.

I hope that helps,

Stephan Watkins

Gesendet:Donnerstag, 19. Dezember 2013 um 00:09 Uhr
Von:jkrie...@mrc-lmb.cam.ac.uk
An:gmx-us...@gromacs.org gmx-us...@gromacs.org
Betreff:Re: [gmx-users] Bin files of g_sham

Youre not asking it to read the bin index file in your command. Maybe that explains what youre seeing?

On 18 Dec 2013, at 13:51, Ankita Naithani ankitanaith...@gmail.com wrote:

Hi Lloyd,

So, my input to g_sham is a file with following lines:

@ title 2D projection of trajectory
@ xaxis label projection on eigenvector 1 (nm)
@ yaxis label projection on eigenvector 2 (nm)
@TYPE xy
0.16750 0.18278
-0.01448 -0.14834
-0.32757 0.22259
-0.33832 0.63817

This file is named AM_12.xvg

and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm

My bin index file has the following lines:

[ 18 ]
7105
[ 19 ]
7104
[ 46 ]
7124
[ 48 ]
7123
[ 49 ]
7106
[ 50 ]
6497
6498
[ 51 ]
6499
6500
[ 52 ]
6496
7103
[ 53 ]
7102
[ 55 ]
6672
[ 75 ]
5745
5749
and so on.

I am not sure how can I look at the default binwidth.

Kind regards,

Ankita

On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:

You need to explain what you are doing better, what you want to do, and
show your input (command line, .xvg lines of input and output as example)
and you might get more help on here. If you read the -h from g_sham, it is
making a single plot from your input, and in this case your .xpm would be a
matrix with bins on a 2D surface with points taken across the entire run,
as an example of what I mean. I believe you can also use a single line
(time, energy as column 2), and get a single line out as well, with a
meaningless landscape still put out as .xpm, etc...look at your binwidth
default, input and what you want out is all I could say at this point. You
might be trying to do something else however...

Stephan
*Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr

*Von:* Ankita Naithani ankitanaith...@gmail.com
*An:* Discussion list for GROMACS users gmx-us...@gromacs.org
*Betreff:* Re: [gmx-users] Bin files of g_sham
I would like to add that maybe the bins store Frame numbers. Because I seem
to have around 21000 frames and I guess I am unable to see a number higher
than that. Apologies for the confusion about earlier number. So, in this
case if I want a confirmation at a particular frame number, how should I go
about that? Could you please help me with that?

Kind regards,

Ankita

On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani
ankitanaith...@gmail.comwrote:

Hi Llyod,

Thank you for your reply. I actually wanted to extract frames
corresponding to the g_sham output. The input for g_sham in my case was
column 1 had time points, column 2 and column 3 had Principal component 1
and Principal component 2 respectively. So, the binning which has been
done, i.e. if I say that the bin number 786 has the following few numbers
like : 3876, 9870, 22002 etc. These should technically correspond to the
time points right which I can then dump using trjconv too maybe.

Also, I am a little confused because if the bins have all the time
points,
I dont seem to find the time points uptil the end

Re: [gmx-users] Bin files of g_sham

2013-12-15 Thread lloyd riggs

I will attempt an answer, however there might be a better response. It depends on your input .xvg (what the first column is) and what you are telling it to do (defualt is time), and if these correspond to your time frames (can be timepoint or siply frame # I believe). g_sham seems (to me) to work like a comand line spread sheet manipulator with some built in functions. If you want a particular frame from a trajectory time point, then use g_traj with the first/last set to the frame you want but theres also 2 other tools that do this the same way...

Stephan Watkins

Gesendet:Sonntag, 15. Dezember 2013 um 14:49 Uhr
Von:Ankita Naithani ankitanaith...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:[gmx-users] Bin files of g_sham

Hi,

I had a query regarding the bin files generated by g_sham.
Does the bin index contain timepoints? i.e. there are 1024 bins so each bin
has a number of time points? And supposes bin 756 has numbers like 3876,
20020, 7896 so these would all correspond to time and we could then dump
the representative frame corresponding to these time points?

I am a little confused as to what is stored in the bins? Timepoints or
frame number and then alternatively how to get the representative
frame/snapshot stored at that specific bin number.

Kind regards,

--
Ankita Naithani
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] Charge correction PME

2013-11-30 Thread lloyd riggs

Sorry to but in on the conversation. Im between computers so cant track it down easy, (on my hard drive) but I did find one older publication comparing gromacs solvent (ion/buffers) effects with plasmon resonance calculated affinities, the results of that single paper showed the closer the solvent ion, etc...to the ones used in the wet experiments, the better the fit between affinity curves (protein-protein). Thus even the older software seemed to represent reality in some ways well...but I never ran across something that broke these down into energy components...thus would like to see the graphs out of curiosity...just a lit search for something I know exists...

Stephan Watkins

Gesendet:Samstag, 30. November 2013 um 18:01 Uhr
Von:Mark Abraham mark.j.abra...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org, Vitaly Chaban vvcha...@gmail.com
Betreff:Re: [gmx-users] Charge correction PME

... but not necessarily any good! See
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html.
I have seen Gerrit present some convincing results since then, but they do
not seem to be in press, yet.

Neutralizing explicitly seems like the right course just about always!

Im never sure why people think extracting an energy component means
anything; extracting part of an intrinsically global one seems even less
likely to mean anything... Do enlighten me! :-)

Mark

On Sat, Nov 30, 2013 at 5:29 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

I might be wrong here, but my expectation is that nowadays you should
not do anything explicitly in this regard. The compensating charge is
automatically applied.

Dr. Vitaly V. Chaban

On Sat, Nov 30, 2013 at 5:14 PM, Benrezkallah Djamila
benrezkal...@gmail.com wrote:
Dear gmx_users,
My question is about the coulomb LR contribution with PME, I cant
access
to davids original post treating this subject in the mailing list (
http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html) if it
exists, because some links are disabled.If any one can send me the page?
Im working on a protein in explicit solvent (water) at different
concentration of salt (NaCl).I need to calculate coulomb LR energy
interaction between some residues and Cl-/Na+.
My question is :should I turn off the charge correction ( when
calculating
electrostatics for no neutral system),and how to do it? or it has a small
contribution to the energy, and I have no worry about it.

I hope find answers in your replies.

respectively,
Djamila Benrezkallah
University of Oran
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Cant 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.
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Cant 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.

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

Diese E-Mail wurde aus dem Sicherheitsverbund E-Mail made in
Germany versendet: http://www.gmx.net/e-mail-made-in-germany
--
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.

Re: [gmx-users] Normal Mode Analysis

2013-11-25 Thread lloyd riggs


I dont know your energy break down, if you look at frames with g_anaeig using -first and -last to set your vector number(s), and then frames set to your time units desired, it will give you something you can look at with vmd or pymol. I have noticed though after the frst 4 or so vectors, it becomes dificult to see movement, as the enrgy break down for even larger proteins starts to become close to single amino acid or very small single atom contributions to the entire energy landscape. Thus hard to spot visually, as the enrgies might be only one or two high energy hydrogen bonds, etc...



Stephan Watkins



Gesendet:Montag, 25. November 2013 um 17:05 Uhr
Von:Sathish Kumar sathishk...@gmail.com
An:Discussion list for GROMACS users gmx-us...@gromacs.org
Betreff:[gmx-users] Normal Mode Analysis

Dear users,

I am trying to do NMA

First i did energy minimization using .mdp file with conjugate gradient
method,

Next i calculated hessian matrix by using integrator = nm

Then i calculated the eigen vectors from 7 to 100 using g_nmeig

to analyze eigen vectors i use the commands

g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
proj-ev1.xvg -extr

ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30


by visuvalizing ev1.pdb, i did not found any motion in the protein.


what is the mistake i have done?

Is it correct procedure for doing NM analysis?

How to analyze the eigen values obtained from hessian matrix?


regards
M.SathishKumar
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.



Diese E-Mail wurde aus dem Sicherheitsverbund E-Mail made in
Germany versendet: http://www.gmx.net/e-mail-made-in-germany
-- 
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.

Re: [gmx-users] How can I tell whether or not Gromacs was compiled with MPI?

2013-11-24 Thread lloyd riggs

Try using the mpi submissions flags with just a test submission, you might have to look at the stats after 15 minutes though, as I do not know what would happen if it was not compiled with mpi (if they work or not), but they would make a noticable difference.

just a suggestion, there might be an easier way.

Stephan Watkins

Gesendet:Sonntag, 24. November 2013 um 23:13 Uhr
Von:Andrew DeYoung adeyo...@andrew.cmu.edu
An:gmx-us...@gromacs.org
Betreff:[gmx-users] How can I tell whether or not Gromacs was compiled with MPI?

Hi,

I am running Gromacs version 4.5.5. However, I did not compile it myself;
the system administrator did many months ago. I have been running
standard MD simulations (i.e., no replica exchange) over the 24 cores that
are available on the node. To run standard MD, I just call mdrun directly
-- without referencing MPI or mpirun (at least not explicitly) -- using a
command like this:

mdrun -v -s topol.tpr -nt 24

>From looking at the old release notes, it looks like this thread-based
parallelization was introduced sometime in version 4.5 (maybe from the
beginning of version 4.5?). As the page
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x says,

Running on a multi-core node now uses thread-based parallelization to
automatically spawn the optimum number of threads in the default build. MPI
is now only required for parallelization over the network.

Now, however, I want to run replica exchange simulations. I have no
experience with such simulations, but the page
http://www.gromacs.org/Documentation/How-tos/REMD says:

REMD with any version of GROMACS requires mdrun compiled with MPI (i.e. not
threading), and that the number of processors be a multiple of the number of
replicas.

But, my question is, how can I tell whether Gromacs was compiled with MPI?
Probably it was not compiled with MPI, since I am using threading, but how
can I be sure?

Thanks so much for your time!

Andrew DeYoung
Carnegie Mellon University

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Cant 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.

--
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.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 106

Re: [gmx-users] conserved energy

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Re: [gmx-users] calculating free energy

Re: [gmx-users] trjconv_d errors

Re: [gmx-users] trjconv_d errors

Re: [gmx-users] Axis

Re: [gmx-users] Version 12

Re: [gmx-users] Membrane simulations

Re: [gmx-users] MD workstation

Re: [gmx-users] protein-ligand complex by gromacs

Re: [gmx-users] g_mindist for hydrophobic interactions

Re: [gmx-users] centering with trjconv

[gmx-users] Membrane simulations

Re: [gmx-users] Membrane simulations

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

Re: [gmx-users] Need some help with membrane simulation

Re: [gmx-users] New Molecule Topology

Re: [gmx-users] (no subject)

Re: [gmx-users] binding sites with MD

Re: [gmx-users] entropy vs time plot

Re: [gmx-users] GPU in Ubuntu

Re: [gmx-users] GPU in Ubuntu

Re: [gmx-users] PEG residue

Re: [gmx-users] binding delta G, H and S for ion-protein

Re: [gmx-users] MD SIMULATIONS ON A CLUSTER

Re: [gmx-users] pca

Re: [gmx-users] Potential energy calculations

Re: [gmx-users] Potential energy calculations

Re: [gmx-users] Potential energy calculations

Re: [gmx-users] Bin files of g_sham

Re: [gmx-users] Bin files of g_sham

Re: [gmx-users] Charge correction PME

Re: [gmx-users] Normal Mode Analysis

Re: [gmx-users] How can I tell whether or not Gromacs was compiled with MPI?

35 matches

Site Navigation

Mail list logo

Footer information