Re: [gmx-users] grommp warning

Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am using option com Is it right As per your

Re: [gmx-users] grommp warning

On 15/08/2012 2:43 PM, rama david wrote: Hi Justin , Thank you for immediate reply and providing the link. But I am wonder for following things... For protein simulation in your lysozyme tutorial we use refcoord_scaling = com In lipid tutorial also same one.. So Is there are any case when to

Re: [gmx-users] grommp warning

Hi Justin , Thank you for immediate reply and providing the link. But I am wonder for following things... For protein simulation in your lysozyme tutorial we use refcoord_scaling = com In lipid tutorial also same one.. So Is there are any case when to use refcoord_scaling no or all .??

Re: [gmx-users] Parameters for bonded interactions

On 15/08/2012 9:46 AM, Sebastien Cote wrote: Dear Gromacs users, In the topology file of the protein, we see every two atoms that share a bond, three atoms that share a bond angle, and four atoms that share a torsion angle. However, the parameters (equilibrium value, energy constant, phase) ar

RE: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

Dear Peter, I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as in Klauda's paper). I will retry with a more solvated membrane.  Would you have any thought on how the NPAT ensemble might affect peptide-membrane interactions like I am studying i.e. peptide is totally

RE: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

Dear Felipe, I will take a lot at this paper. Thanks! Sebastien  > Date: Tue, 4 Aug 012 9::8::7 +200< > From: luis.pinedadecas...@lnu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] CHARMM6 - Smaller Area per lipid for POPE - Why? > > Hi Sébas

[gmx-users] Parameters for bonded interactions

Dear Gromacs users, In the topology file of the protein, we see every two atoms that share a bond, three atoms that share a bond angle, and four atoms that share a torsion angle. However, the parameters (equilibrium value, energy constant, phase) are not explicitly shown as Gromacs fetch them

[gmx-users] RE: RE: RE: Doubts over g_lie usage

There are different methods used to calculate the electrostatics, RF-0 is one. 7.3.10 in the manual. You can just use the -rerun flag in mdrun, after creating an appropriate .tpr file with grompp and a new .mdp file. If I understand it properly this effectively calculates single point interacti

RE: [gmx-users] a residue move in extremely large scale in MD

You are missing a major conceptual principle of MD here. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Read manual, section 3.2 Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade

Re: [gmx-users] PLUMED-GROMACS force constant, angle unit

On 8/14/12 2:15 PM, tarak karmakar wrote: Hi David, Thanks for the reply. But I rechecked the paper [ http://www.sciencedirect.com/science/article/pii/S0009261408007975] as I mentioned earlier, the unit of the harmonic force constant for the dihedral is kcal/mol/deg^2. Again if the force const

Re: [gmx-users] PLUMED-GROMACS force constant, angle unit

Hi David, Thanks for the reply. But I rechecked the paper [ http://www.sciencedirect.com/science/article/pii/S0009261408007975] as I mentioned earlier, the unit of the harmonic force constant for the dihedral is kcal/mol/deg^2. Again if the force constant unit is independent of degree or radian th

Re: [gmx-users] simulation

Thanks for the link.   Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Tuesday, August 14, 2012 10:25 PM Subject: Re: [gmx-users] simulation On 8/14/12 1:49 PM, Shima Arasteh wrote: > > > Hi all, > > I'm simu

Re: [gmx-users] simulation

On 8/14/12 1:49 PM, Shima Arasteh wrote: Hi all, I'm simulating a system of POPC and water for 50 ns. I set the job but it interrupted in the middle of the job due to cluster problem and I got the results up to 40 ns. Is it possible to continue it for the last 10 ns and not doing the sim

[gmx-users] simulation

Hi all, I'm simulating a system of POPC and water for 50 ns. I set the job but it interrupted in the middle of the job due to cluster problem and I got the results up to 40 ns.  Is it possible to continue it for the last 10 ns and not doing the simulation from the beginning? Please guide me.

[gmx-users] PhD position in Göttingen/Germany

Dear simulators, we have a PhD position available in the Computational Molecular Biophysics group in Göttingen (Germany). Please have a look here for more details: http://cmb.bio.uni-goettingen.de/jobs.html Thank you, Jochen -- --- Dr. Jochen

Re: [gmx-users] grommp warning

On 8/14/12 11:28 AM, rama david wrote: Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... A simple search of the list archive turns up lots of discussions like thi

Re: [gmx-users] grommp warning

Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... With best wishes and regards Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Re: [gmx-users] grommp warning

On 8/14/12 11:15 AM, rama david wrote: Dear shima and Justin, These error is come on Gromacs 4.5.5 at the time of NPT if refcoord_scaling option not used.. But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling option at npt Is any one else has same experience? I really s

Re: [gmx-users] grommp warning

Dear shima and Justin, These error is come on Gromacs 4.5.5 at the time of NPT if refcoord_scaling option not used.. But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling option at npt Is any one else has same experience? I really surprised by my observation With best

Re: [gmx-users] checkpoint file

Hi Juliette , If your data is more and because of that may be -append not support you. Then these may be help you .. mdrun -v -deffnm -s -cpi cpt See carefully the output and check the time at which the run start..Is the starting time point matches your crash point. lastly when run c

Re: [gmx-users] Questions regarding Polarization Energy Calculation

Thanks Mark for your reply. I was trying to use Single-Point Energy Calculation as you advised in your first reply but for most of the files the simulation failed because I was using the original .pdb files in the mdrun command. Anyways. I really appreciate your help. Thanks again, Jesmin On Tue,

Re: [gmx-users] PLUMED-GROMACS force constant, angle unit

On 2012-08-14 14:27, tarak karmakar wrote: Dear All, In the manual I see the unit of the k{theta} is kJ/mol/rad^2. But Neale et al in Chemical Physics Letters 460 (2008) 375–381 has applied the harmonic restraints with a force constant of 0.0364 kcal/mol/deg^2 for the phi and psi dihedral angle

[gmx-users] box of simulation

Dear Mark, Thank you very much from your help. Best Regards Sara - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Tuesday, August 14, 2012 2:44 PM Subject: Re: [gmx-users] box of simulation On 14/08/2012 6:55 PM, mohammad agha wrote: > Dear Ma

Re: [gmx-users] Ions topology

Dear Mark, Thank you for your reply. I am using gromos53a6 force field. On Tue, Aug 14, 2012 at 11:16 AM, Mark Abraham wrote: > On 14/08/2012 7:45 PM, Ankita naithani wrote: >> >> Dear All, >> >> I wanted to ask that from where can I get the topologies and >> co-ordinate information for Mg and

Re: [gmx-users] Ions topology

On 14/08/2012 7:45 PM, Ankita naithani wrote: Dear All, I wanted to ask that from where can I get the topologies and co-ordinate information for Mg and K ions? For the ligands, I could get it from PRODRG software as suggested in the tutorial but my protein needs the crucial ions Mg and K before

Re: [gmx-users] box of simulation

On 14/08/2012 6:55 PM, mohammad agha wrote: Dear Mark, Thank you very much from your help. I used from genbox to place solvent molecules. my question is : In the NPT ensemble, for equilibrium, may the box become smaller than definite sizes before equilibrium(for example 2nm become smaller)

[gmx-users] Ions topology

Dear All, I wanted to ask that from where can I get the topologies and co-ordinate information for Mg and K ions? For the ligands, I could get it from PRODRG software as suggested in the tutorial but my protein needs the crucial ions Mg and K before I can begin with my simulations. Best Wishes,

[gmx-users] box of simulation

Dear Mark, Thank you very much from your help. I used from genbox to place solvent molecules. my question is : In the NPT ensemble, for equilibrium, may the box become smaller than definite sizes before equilibrium(for example 2nm become smaller) and if yes, why haven't been placed molecules i

[gmx-users] box of simulation

Thank you very much. Best Regards Sara - Original Message - From: Emanuel Birru To: 'mohammad agha' ; Discussion list for GROMACS users Cc: Sent: Tuesday, August 14, 2012 12:46 PM Subject: RE: [gmx-users] Fw: box of simulation I am not sure whether a pressure coupling equilibration

Re: [gmx-users] Fw: box of simulation

On 14/08/2012 6:16 PM, Emanuel Birru wrote: I am not sure whether a pressure coupling equilibration enlarges the specified box size of the simulation :) It can. if the box size is not appropriate to maintain the pressure coupling the simulation probably blow up instead of adjusting the b

Re: [gmx-users] box of simulation

On 14/08/2012 5:27 PM, mohammad agha wrote: Dear Gromacs Users: When I want to place 12000 solvent molecule in the box (15*15*15) it say: What's "it"? genbox? grompp? You can't be helped effectively if you don't provide your command lines that produce output, and/or a description of wha

Re: [gmx-users] a residue move in extremely large scale in MD

On 14/08/2012 5:54 PM, Acoot Brett wrote: Dear All, Thanks for the reply. Then is any single trjconv command available before viewing the trajectory file, or before extracting the xtc file, with that command all the fraud caused by the PBC effect will be got rid of? I linked a page with a wo

RE: [gmx-users] Fw: box of simulation

I am not sure whether a pressure coupling equilibration enlarges the specified box size of the simulation :) if the box size is not appropriate to maintain the pressure coupling the simulation probably blow up instead of adjusting the box size to a bigger one. For more info check the following

[gmx-users] Fw: box of simulation

Hi Emanuel, Thank you very much from your response. yes, my topology is correct. It means that it isn't one problem and it is natural.yes? This question is because of in the most of papers has been said that the box is enlarged with equilibrium but my box become smaller! Best Regards Sara -

[gmx-users] box of simulation

Hi Emanuel, Thank you very much from your response. It means that it isn't one problem and it is natural.yes? Best Regards Sara - Original Message - From: Emanuel Birru To: 'mohammad agha' ; 'Discussion list for GROMACS users' Cc: Sent: Tuesday, August 14, 2012 12:06 PM Subject: RE

Re: [gmx-users] a residue move in extremely large scale in MD

Dear All, Thanks for the reply. Then is any single trjconv command available before viewing the trajectory file, or before extracting the xtc file, with that command all the fraud caused by the PBC effect will be got rid of? In addition, the "box" in the e-mail of Dr Dallas Warren should be the

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

Hi Sébastien, I found the following paper very instructive about this issue (simulated areas per lipid in bilayers): Jensen, M. et al. Simulations of a membrane anchored peptide: structure, dynamics, and influence on bilayer properties. Biophys. J. (2004)86, 3556-75 Take maybe a look at it,

RE: [gmx-users] box of simulation

Hi Sara, The number of molecules in your .gro file and .top file should be the same. That means when you want to add 12000 solvent molecules, change the number of solvent molecules in your topology file to 12000. The total number of your solvent and solute molecules in you topology and coordina

[gmx-users] box of simulation

Dear Gromacs Users: When I want to place 12000 solvent  molecule in the box (15*15*15)  it say: number of coordinates in coordinate file (ctacyc.gro, 28794) does not match topology (topol.top, 37950) it means that I should enlarge the box to place all of solvent molecules into th

[gmx-users] box of simulation

Dear Gromacs Users: When I want to place 12000 solvent  molecule in the box (15*15*15)  it say: number of coordinates in coordinate file (ctacyc.gro, 28794) does not match topology (topol.top, 37950) it means that I should enlarge the box to place all of solvent molecules into that.

Re: [gmx-users] Parrinello-Rahman with surface-tension coupling

Thanks for the advice, Mark! I did exactly this experiment with the same expectations before posting my query. I didn't get any complaint neither from grompp nor from mdrun, what doesn't necessarily mean that this combination is implemented. I just noticed that during equilibration results det