[gmx-users] Energy minimization by keeping heavy atom fixed

I have a protein structure determined by x-ray crystallography method where hydrogen atoms were missing. I have added hydrogen atom. Now i need to do energy minimization of this protein by keeping the heavy atom fixed at their crystallographic position. How can I manage which atoms to be fixed and

Re: [gmx-users] Energy minimization by keeping heavy atom fixed

- Original Message - From: priyabrata panigrahi priyabra...@gmail.com Date: Thursday, August 26, 2010 17:09 Subject: [gmx-users] Energy minimization by keeping heavy atom fixed To: gmx-users@gromacs.org I have a protein structure determined by x-ray crystallography method where

[gmx-users] following_change_native_contact

Dear All How can I follow the changes in native contacts of protein unfolding trajectory. Is it g_mdmat, if so then how to analyze the results obtained from this command. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

RE: [gmx-users] How to calculate the distances

Dear Mark, It works. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, August 26, 2010 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How

[gmx-users] question about how to jump into an archived discussion...

Hello everyone, I don't get understand the following. I found an archive of a useful discussion, and I want to jump in with my own comment. But the button at the bottom of the page evidently only allows me to email the person directly. It says reply via email to: [person]. If I send the person an

Re[2]: [gmx-users] initial velocities analysis

Hi, Justin. I'm also interested in this question. Could you make clear: Anna Marabotti wrote: ... - is there a way to check for the velocities or for the random seed used? I had a look at the .log file but I didn't find the information. g_traj generated a very big file, and presently I

Re: Re[2]: [gmx-users] initial velocities analysis

- Original Message - From: Dmitri Dubov ddu...@ngs.ru Date: Thursday, August 26, 2010 18:17 Subject: Re[2]: [gmx-users] initial velocities analysis To: Discussion list for GROMACS users gmx-users@gromacs.org font style=font-style: normal; font-weight: normal; background-color:

[gmx-users] Surface tension coupling

Hi, I am trying to obtain the surface tension for the hexane-water interface. I used Gromacs 4.0.7. A simulation where I keep the X-Y dimensions fixed and let z fluctuate yields the following output: Energy Average RMSD Fluct. Drift Tot-Drift

[gmx-users] Dipeptide generation problem

Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent and produces error when I

Re: [gmx-users] Dipeptide generation problem

Eudes Fileti wrote: Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent

[gmx-users] pbc atom

Gavin, I recall mentioning gen_vel=no with temperature coupling as a possible problem a while ago (the problem is that the initial forces become initial velocities and then those get scaled up and what you have are velocities and not temperatures -- read about the flying ice cube problem).

[gmx-users] RE: Molecule out of pbc box

Hi, Does anyone know if there is a way to put a molecule back in the pbc box in gromacs. I am visualizing my sims in vmd and the molecule keeps going out of the box. Is it normal or an artifact in vmd, is there a way to put the molecule back in the box? please let me know. Thanks, Nimesh --

Re: [gmx-users] RE: Molecule out of pbc box

Nimesh Jain wrote: Hi, Does anyone know if there is a way to put a molecule back in the pbc box in gromacs. I am visualizing my sims in vmd and the molecule keeps going out of the box. Is it normal or an artifact in vmd, is there a way to put the molecule back in the box? please let me

[gmx-users] Molecule out of pbc box

Dear Nimesh: trjconv -f orig.xtc -s my.tpr -o new.xtc -pbc atom to get the help information: trjconv -h Normally, you might not get an answer to this one since it's the most commonly asked question. The users list search is, however, not working right now so I thought I'd pass along the

Re: [gmx-users] RE: Molecule out of pbc box

- Original Message - From: Nimesh Jain nimeshjain2...@u.northwestern.edu Date: Friday, August 27, 2010 0:15 Subject: [gmx-users] RE: Molecule out of pbc box To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, Does anyone know if there is a way to put a molecule back in

[gmx-users] gromacs users list search for molecule returns zero results

I think that there is some problem with the users list search on the gromacs page: http://www.gromacs.org/Support/Mailing_Lists/Search A gromacs users list search for molecule returns zero results. A search for gromacs does return lots of results. A google search for gromacs and molecule

[gmx-users] g_sas = protein interface = HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface From David = If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] pbc atom

O.K Chris Thanks for all your help. I am actually considering removing the thermostat all together seeing as my system is quite small. I have also started using gen_vel = yes (no matter how much I think my system is in equilibrium). One quick question (perhaps its silly). When you say the initial

Re: [gmx-users] Dipeptide generation problem [Justin]

: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html -- Message: 3 Date: Thu, 26 Aug 2010 08:36:24 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Dipeptide generation problem To: Discussion list

[gmx-users] making index file

Hello Justin, Please let me explain my naive procedure to make index file so that you can make comment. I have created the top file for a single solvent molecule. Then removed [system] , [molecule] directives as well as #ffgmx.itp. The [molecule type] is named 'solvent''. I got a sample itp file

Re: [gmx-users] Dipeptide generation problem [Justin]

- Original Message - From: Eudes Fileti fil...@ufabc.edu.br Date: Friday, August 27, 2010 2:15 Subject: Re: [gmx-users] Dipeptide generation problem [Justin] To: gmx-users@gromacs.org Olá Justin, thank you for responding to my post. I had tried what you mentioned before. All I get

RE: [gmx-users] Dipeptide generation problem [Justin]

/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html -- Message: 3 Date: Thu, 26 Aug 2010 08:36:24 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Dipeptide generation problem To: Discussion list for GROMACS users gmx-users

Re: [gmx-users] making index file

- Original Message - From: Moeed lecie...@googlemail.com Date: Friday, August 27, 2010 2:21 Subject: [gmx-users] making index file To: gmx-users@gromacs.org Hello Justin, Please let me explain my naive procedure to make index file so that you can make comment. I have created the

[gmx-users] minima

g_anaeig command give some minimum or maximum value are these value energy minima and maxima for extreme 2 frame structures? eigenvector Minimum Maximum value time value time 1 -9.162661 99.0 2.682097 9450.0 2

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more

[gmx-users] Re: making index file

Moedd - Why don't you like interactive commands of make_ndx? It is easy to form any atom groups based on your GRO file content... Vitaly -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester, Rochester, NY, U.S.A. Please let me explain my naive procedure to make index

[gmx-users] AFM Pulling Simulations

Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations

Re: [gmx-users] AFM Pulling Simulations

Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the

Re: [gmx-users] AFM Pulling Simulations

Quoting Justin A. Lemkul jalem...@vt.edu: Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few

Re: [gmx-users] minima

Hi Pawan, These are the maximum and minimum projections on the eigenvectors. They are very unlikely to correspond to energy minima, as minima will be modal. Think of a pendulum, projecting the position on the floor. The extreme projections actually correspond to states of higher (potential)

RE: RE: [gmx-users] Dipeptide generation problem [Justin, Mark, Osmair]

CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html -- Message: 3

Re: [gmx-users] Dipeptide generation problem [Justin, Mark, Osmair]

attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100826/0cfce19f/attachment-0001.html -- Message: 3 Date: Thu, 26 Aug 2010 08:36:24 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem

[gmx-users] pbc atom

velocities are not taken from the .gro as far as I know. You can get them from the .trr if you also use a .edr. If you want to check, then do a run for only 1 ps and save your .edr every timestep. Then run g_energy and look at the temperature. I am not sure that a constant energy

[gmx-users] AFM Pulling Simulations

Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short period of time, then the stage is set for

Re: [gmx-users] dipole moment of molecule of trans and cis azobenzene ?

On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. and where do you get the charges from? It is supposed that the real molecule of trans-azobenzene has a lower dipole

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

HI The charges of azobenzene from the authors, who made the QM/MM simulations and fit some experimental data about the azobenzene. Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom

[gmx-users] g_sas = protein interface = HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface From David = If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

HI From David = dipole moment = mu = sum_i q r. is that sum of partial charges * r ? what is the r ? Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation.

[gmx-users] g_sas = calculate the SASA for each residues ?

Hi How can I calculate the SASA for each residue ? From Manual = The program will ask for a group for the surface calculation and a group for the output. When I issue the command = g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg = Gromacs will pick Residue1.ndx as both a group for

Re: [gmx-users] g_sas = calculate the SASA for each residues ?

Chih-Ying Lin wrote: Hi How can I calculate the SASA for each residue ? From Manual = The program will ask for a group for the surface calculation and a group for the output. When I issue the command = g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg = Gromacs will pick

Re: [gmx-users] How to tell if the molecule is correctly reduced?

Thanks Roland and Mark for your input.I did pdb2gmx -ss and checked the top file where the Cys are represented as CYSH, but when I loaded the generated pdb file in vmd, I can still see the original dsulfides bond, and each sulfur is protonated. Is this an artifact? Is there another way to

Re: [gmx-users] g_sas = protein interface = HALF of ( A+B-AB) ?

Hi, the interface is now A + B - AB WHy not HALF of (A+B-AB)  ? You are right. A + B - AB gives the Buried Surface Area, which is the amount of surface that gets excluded from the solvent by complexation (and consequently is twice the size of the interface). :) Tsjerk -- Tsjerk A.