Re: [gmx-users] MD simulation of metalloprotein

On 4/28/15 1:29 AM, Biplab Ghosh wrote: Dear All, I am a beginner in MD and started with Gromacs. I would like to simulate the dynamics of a homo-dimeric protein containing 2 Mn atoms at the active site. I would appreciate any sorts of help in this regards, e.g., please share your experience

Re: [gmx-users] Number Error in XTC file

Hi, Typically that means you're reading a trajectory of size 2GB on a filesystem that can't do that (e.g. a 32-bit one). Mark On Tue, Apr 28, 2015 at 4:20 PM Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got the error in the end of trajectory converting: Magic Number Error in XTC

Re: [gmx-users] Number Error in XTC file

Dear Mark, Many thanks for your answer. Is there anyway to overcome this? Regards, Jennifer On Tue, Apr 28, 2015 at 4:26 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Typically that means you're reading a trajectory of size 2GB on a filesystem that can't do that (e.g. a 32-bit one).

[gmx-users] contribution of inter-molecular distance restraints to the virial

Hi, we use half-harmonic distance restraints between COM of a solute and a number of waters around it. Does Gromacs (gromacs-4.6.3) account for the contribution of these inter-molecular distance restraints to the virial? Where can it be found/included in the code? In disre.c ? We found the

Re: [gmx-users] Number Error in XTC file

If that's the problem, use a machine with a real file system ;-) Mark On Tue, Apr 28, 2015 at 4:34 PM Jennifer Vo quyvio...@gmail.com wrote: Dear Mark, Many thanks for your answer. Is there anyway to overcome this? Regards, Jennifer On Tue, Apr 28, 2015 at 4:26 PM, Mark Abraham

[gmx-users] Number Error in XTC file

Dear All, I have got the error in the end of trajectory converting: Magic Number Error in XTC file (read -335790888, should be 1995) trjconv -s md-1.tpr -f md-300ns-wat.xtc -o md_CA.pdb -n index_8pro.ndx -pbc mol -ur compact -center -skip 1000 Is there anybody know what`s the error about? Many

Re: [gmx-users] on rlist

On 4/27/15 10:06 PM, Brett wrote: Dear All, In the MD mdp file for the old version of on-line tutorials for lysozyme, in the neighbor search, there is an item rlist, but in the MD mdp file for the new version of on-line tutorials for lysozyme, in the neighbor search, there is no item rlist.

Re: [gmx-users] MD simulation of metalloprotein

Hi, we have determined the Mn2+ OPLSA sigma and epsilon parameters in http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/suppinfo following the procedure reported here http://pubs.acs.org/doi/abs/10.1021/jp064835t hope it helps and On 28/04/2015 14:12, Justin Lemkul wrote: On

[gmx-users] Energy minimization error for electroporation simulation of DPPC membrane

Hi all, I am a beginner to GROMACS and MD simulations in general. I’m trying to model electroporation in a DPPC membrane but I am having issues with the energy minimization step. I am basing my approach on the one followed in Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial (

[gmx-users] Charge of the system

Dear allI am using gromacsto simulate ligand bonding to an enzyme. I have two problems withcharge of system: 1) after making topology file for ligand using prodrug, I saw itsnet charge was -0.4. how can I neutralize it?2) I used this topology parameters of ligand to continuesimulation steps.

Re: [gmx-users] NMA with gromacs trajectory

Hi Rajan, NMA/GNM is performed on a single structure, not on a trajectory. NMA can be performed with Gromacs, but GNM/ENM is not possible, AFAIK. Cheers, Tsjerk On Apr 28, 2015 5:07 PM, rajan kumar choudhary rajugunju...@gmail.com wrote: ​Dear all, Is it possible to perform Normal mode

[gmx-users] NMA with gromacs trajectory

​Dear all, Is it possible to perform Normal mode analysis and GNM analysis with gromacs trajectory file in GROMACS or somewhere else. any help in this regard will be very appreciated. ​ ​thank you all​ -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of

Re: [gmx-users] Protein fragments during production simulation

Hi Tsjerk, Thank your for your help. I could get over the issue. :) Regards, Sapna. On Tue, Apr 28, 2015 at 11:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sapna, Check http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cheers, Tsjerk On Apr 28, 2015

Re: [gmx-users] Charge of the system

On 4/28/15 11:14 AM, Emran Heshmati wrote: Dear allI am using gromacsto simulate ligand bonding to an enzyme. I have two problems withcharge of system: 1) after making topology file for ligand using prodrug, I saw itsnet charge was -0.4. how can I neutralize it?2) I used this If the net

Re: [gmx-users] Energy minimization error for electroporation simulation of DPPC membrane

On 4/28/15 8:14 AM, Abhijit Jassem wrote: Hi all, I am a beginner to GROMACS and MD simulations in general. I’m trying to model electroporation in a DPPC membrane but I am having issues with the energy minimization step. I am basing my approach on the one followed in Dr. Justin Lemkul’s

Re: [gmx-users] Epsilon-rf

If I use PME there's no need to find epsilon-rf, but I have to change some other parameters. I will try it. Thank you very much Alex! On Tue, Apr 28, 2015 at 11:31 AM, Alex nedoma...@gmail.com wrote: With reaction-field-zero, the only option is epsilon-rf=0. That aside, if the nanotube is

[gmx-users] Saxs guided MD

Good Afternoon, Recently i saw in a paper that SAXS guided MD was implemented in Gromacs. Here is the paper - http://pubs.acs.org/doi/full/10.1021/ct5009735 I could not find any info on this. Does anyone have any information about this subject? Thank you, Tiago -- Gromacs Users mailing list *

Re: [gmx-users] Molecule specific explosion

Hi Mark, Thanks for the reply. In my previous message, one molecular component of my liquid solution greatly-deforms (explodes) on energy minimization. I have examined the topology and everything seems in order. No warnings were generated by grompp or mdrun. Here are my minimization settings:

Re: [gmx-users] Epsilon-rf

That's a pretty poorly formed question, including the part where you actually calculate the epsilon-rf value. Can you please try again with a description of your system? Alex MK Dear all, MK I use reaction-field-zero as the coulombtype for my system. I wonder how I MK should choose the right

Re: [gmx-users] Epsilon-rf

With reaction-field-zero, the only option is epsilon-rf=0. That aside, if the nanotube is small, i would use cut-off electrostatics with coulomb-cutoff comparable to the length of the tube. If the tube is long, I would use standard pme. I would be extremely careful about using truncated

[gmx-users] Epsilon-rf

Dear all, I use reaction-field-zero as the coulombtype for my system. I wonder how I should choose the right epsilon-rf. How can I calculate the dielectric constant in the system? Thank you. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Molecule specific explosion

Hi, What happens when you use this topology on a single molecule? Other standard techniques for diagnosing at http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Tue, Apr 28, 2015 at 8:09 AM, Eric Smoll ericsm...@gmail.com wrote: Hi Mark, Thanks for the reply. In my previous

Re: [gmx-users] Epsilon-rf

Also, reaction-field-zero, as described here http://manual.gromacs.org/online/mdp_opt.html which _only_ works with epsilon-rf=0. Any particular reason for doing this to your electrostatics? Alex MK Dear all, MK I use reaction-field-zero as the coulombtype for my system. I wonder how I MK