[gmx-users] Error after trjconf processing

Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on

[gmx-users] random seed in molecular dynamics

hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -th

[gmx-users] rotation of a ligand

Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which tool should I use? g_order, g_chi, g_dih? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re: [gmx-users] Temperature for individual amino acid residues

Thanks for your reply and suggestions. On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul wrote: > > > On 5/2/13 10:28 AM, bipin singh wrote: > >> Thanks for the reply. >> I have seen the link. As given in the link that we need to multiply the >> temperature by (3N-Ncons)/3N. Please let me know if I

Re: [gmx-users] vacum simulation

many thanks to all of you. I have decreased the time step. Simulation has finished in right conditions On 3 May 2013 03:06, Dr. Vitaly Chaban wrote: > LINCS doesn't like your system... or your system doesn't like LINCS... > > You can decrease the time-step as the simplest action. > > Dr. Vitaly

Re: [gmx-users] issue in replica exchange

Are confirming that you reproduce the problem with gmx-4.6.1 or simply summarizing in case we lose track :)) On May 2, 2013, at 23:31, Michael Shirts wrote: > So to summarize -- the problem appears to be with particle decomposition. > > On Thu, May 2, 2013 at 4:15 PM, XAvier Periole wrote: >

[gmx-users] distance of pull group 1 is larger than the box size

Hello sir I got the following error while running pulling mdrun -s pull.tpr "distance of pull group 1 is larger than the box size" I request you to kindly guide me in overcoming the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer & Epigenetics) Department

[gmx-users] constant protonation state MD

Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users maili

Re: [gmx-users] issue in replica exchange

So to summarize -- the problem appears to be with particle decomposition. On Thu, May 2, 2013 at 4:15 PM, XAvier Periole wrote: > > I'll look at the 4.6.1 version next week, I could install it but I got a > conflict between the environmental variable defining openMP variable but I > turned it o

Re: [gmx-users] issue in replica exchange

I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On Ma

Re: [gmx-users] where can be obtain circled lipids bilayer?

On 02.05.2013 18:32, Albert wrote: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png As has already been said by others, this is not really a "circled lipid bilayer" but rather a lipid vesicle of very very s

Re: [gmx-users] issue in replica exchange

Some good news … The tpr files provided by Simone do NOT show abnormal behaviour! This good news :)) However after turning ON the particle decomposition option to mdrun (-pd) I got a warnings of water not being able to be settled and a crash. This was still with Simone's trips … I took that

Re: [gmx-users] where can be obtain circled lipids bilayer?

On 5/2/13 2:16 PM, Jesper Sørensen wrote: The shape is a sphere not a circle, what the picture is showing is a cut through the vesicle. Have you googled lipid vesicles? I don't know of a place that will have template systems like this for you. But you should be able to get these by making a l

Re: [gmx-users] where can be obtain circled lipids bilayer?

The shape is a sphere not a circle, what the picture is showing is a cut through the vesicle. Have you googled lipid vesicles? I don't know of a place that will have template systems like this for you. But you should be able to get these by making a large enough system with enough lipids to form

Re: [gmx-users] GPU job often stopped

the problem is still there... :-( On 04/29/2013 06:06 PM, Szilárd Páll wrote: On Mon, Apr 29, 2013 at 3:51 PM, Albert wrote: >On 04/29/2013 03:47 PM, Szilárd Páll wrote: >> >>In that case, while it isn't very likely, the issue could be caused by >>some implementation detail which aims

Re: [gmx-users] vacum simulation

LINCS doesn't like your system... or your system doesn't like LINCS... You can decrease the time-step as the simplest action. Dr. Vitaly Chaban On Thu, May 2, 2013 at 2:40 PM, Souilem Safa wrote: > Dear Gromacs users , > I did the simulation of a single molecule in vacum. I have choose

Re: [gmx-users] where can be obtain circled lipids bilayer?

On Thu, May 2, 2013 at 6:32 PM, Albert wrote: > Hello: > > I've got a question about where can be obtain circled lipids bilayer? > > > like shown here: > > http://wwwuser.gwdg.de/~**ggroenh/membed/vesicle.png > > 1) When packing parameter of t

[gmx-users] where can be obtain circled lipids bilayer?

Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search t

Re: [gmx-users] Exdending

On 5/2/13 11:01 AM, Dubi wrote: Dear Gromacs Community, I m in the situation where I have a trajectory that started in a geometric position "A" and ended in position "B". If I hit a new mdrun with the "-append" extension, than the trr output is the old trajectory together with the new one whic

[gmx-users] Exdending

Dear Gromacs Community, I m in the situation where I have a trajectory that started in a geometric position "A" and ended in position "B". If I hit a new mdrun with the "-append" extension, than the trr output is the old trajectory together with the new one which starts at position "B". Unfortunat

Re: [gmx-users] Temperature for individual amino acid residues

On 5/2/13 10:28 AM, bipin singh wrote: Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. "N" is the total number of protein atoms and "Ncons" will

Re: [gmx-users] Temperature for individual amino acid residues

On 5/2/13 10:28 AM, bipin singh wrote: Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. "N" is the total number of protein atoms and "Ncons" will

Re: [gmx-users] Temperature for individual amino acid residues

Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. "N" is the total number of protein atoms and "Ncons" will be equal to total number of constrains. 1)

Re: [gmx-users] vacum simulation

Thank you very much On 2 May 2013 22:00, Justin Lemkul wrote: > > > On 5/2/13 8:57 AM, Souilem Safa wrote: > >> Thank you for your quick answer >> I have joined here my mdp file and the toplogy one also. >> > > The mailing list does not accept attachments. Please copy and paste the > text into

Re: [gmx-users] vacum simulation

On 5/2/13 8:57 AM, Souilem Safa wrote: Thank you for your quick answer I have joined here my mdp file and the toplogy one also. The mailing list does not accept attachments. Please copy and paste the text into an email. We may not need the whole topology, but a description of what you're

Re: [gmx-users] vacum simulation

Thank you for your quick answer I have joined here my mdp file and the toplogy one also. Should I increase the time step? I'm sorry I'm new in MD On 2 May 2013 21:48, Erik Marklund wrote: > You seem to be using a 2 fs time step. It's difficult to achieve stable > integration using 2 fs time st

Re: [gmx-users] vacum simulation

You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters. Erik On 2 May 2013, at 14:40, Souilem Safa wrote: > Dear Gromacs users , > I did the simulation of a single mo

Re: [gmx-users] vacum simulation

On 5/2/13 8:40 AM, Souilem Safa wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open

[gmx-users] vacum simulation

Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun s

Re: [gmx-users] issue in replica exchange

Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole wrote: > > You mean working with or working on the code? > > I'll try gmx-4.6.1 > > On M

Re: [gmx-users] issue in replica exchange

You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts wrote: > Quick check here -- is 4.6 behaving correctly? I actually spent some > time working on REMD in 4.6, and it seems to be behaving correctly in > my hands with temperature and p

Re: [gmx-users] issue in replica exchange

Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham wrote: > On Thu, May 2

Re: [gmx-users] issue in replica exchange

On Thu, May 2, 2013 at 12:58 PM, XAvier Periole wrote: > > I saw that redmine report, which could be related but it seems to happen > only for runs done outside the domain and particle decompositions. > > I'll fill up a red mine. > > Anything I could do to help speeding the fix? > What'd be real

Re: [gmx-users] issue in replica exchange

I mean tpr files not tar! Autocorrection is sometimes funny :)) On May 2, 2013, at 2:11 PM, XAvier Periole wrote: > > Could you send me a set of tar files that I could look at things the same way > I do with my system? I would guess that 6 tar files where you same energies > and print log fi

Re: [gmx-users] issue in replica exchange

Could you send me a set of tar files that I could look at things the same way I do with my system? I would guess that 6 tar files where you same energies and print log file every step but xtc and trr files not that often would be really cool. You can send them directly to my email (x.peri...@

Re: [gmx-users] issue in replica exchange

Yes, my system is described at atomic level. No, I can't see any "strange" value around exchanges. I analyzed only a very little number of trajectories, but temperature, volume, potential energy, pressure seem all to be around normal fluctuations. 2013/5/2 XAvier Periole > > Did you look at som

Re: [gmx-users] surrounding a peptide by ions of magnesium

On 5/2/13 7:33 AM, Mohan maruthi sena wrote: Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? genbox -ci -nmol You will need a coordinate file for a single Mg2+ ion to be inserted, which is trivia

Re: [gmx-users] surrounding a peptide by ions of magnesium

Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? Thanks, Mohan On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul wrote: > > > On 5/2/13 12:38 AM, Mohan maruthi sena wrote: > >> Hi all, >> I hav

Re: [gmx-users] surrounding a peptide by ions of magnesium

On 5/2/13 12:38 AM, Mohan maruthi sena wrote: Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we

Re: [gmx-users] Temperature for individual amino acid residues

On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it

Re: [gmx-users] issue in replica exchange

I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? On May 2, 2013, at 11:53 AM, Mark Abraham wrote: > On Wed, May 1, 2013 at 10:24

Re: [gmx-users] issue in replica exchange

Did you look at some data like temperature/pressure/box size/Epot as a function of time and especially around some exchanges? Your system is atomistic I presume. On May 2, 2013, at 12:38 PM, Simone Conti wrote: > I'm running remd in NPT ensemble for a small peptide and all is ok if the > max

Re: [gmx-users] issue in replica exchange

I'm running remd in NPT ensemble for a small peptide and all is ok if the maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. If I try to add repl

Re: [gmx-users] issue in replica exchange

On Wed, May 1, 2013 at 10:24 PM, XAvier Periole wrote: > > Ok here is my current status on that REMD issue. > > For info: I use > Temperature: v-rescale, tau_t = 2.0 ps > Pressure: berendsen, tau_p = 5.0 ps, > time step: dt=0.002 - 0.020 fs, > COM removal on for bilayer/water separately > > The s

Re: [gmx-users] minimization of particular residue/atom

That procedure can work. That it works in your case surprises me a little. :-) Mark On Thu, May 2, 2013 at 11:25 AM, gromacs query wrote: > Dear Mark, > > I found a simple(est) fix to this problem. Say in my case I was getting > error inf on atom 4281 ( Maximum force =inf on atom

[gmx-users] Re: PMF calculation between protein and ligand

If you refer to Justin's tutorial, you can use it for every system, where the reaction coordinate is the distane between two parts of the system. You probably need to make some little adjustments, but in the end it doesn't matter if you pull two proteins apart, or protein+ligand, 2 water molecu

Re: [gmx-users] minimization of particular residue/atom

Dear Mark, I found a simple(est) fix to this problem. Say in my case I was getting error inf on atom 4281 ( Maximum force =inf on atom 4281) What I did: In gro file for atom number 4281 I edited one of its coordinate just 0.1nm that is 1 Angs e.g. 6.518 to 6.618 (I did for x, but

RE: [gmx-users] help with g_hydorder and g_polystat

That's ok. Thank you for your help. In the meantime, I might see if g_h2order is a good substitute for g_hydorder. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sen

Re: [gmx-users] g_msd for many molecules

Hi, if you want to calculate the MSD of several molecules, say nrmol, without using the -mol option, which I do not know is still broken, you can do this in three simple steps: 1. Convert your trajectory with trjconv and the option -pbc whole 2. Create an index file, that contains groups, whic

[gmx-users] Re: local pressure

Hi everybody, There is some more information about the issue in the MARTINI web page: http://md.chem.rug.nl/cgmartini/index.php/3d >From there you can download the tools to analyze the binary file localpressure.dat which is given out by a gromacs code. There is more information in the README fil

Re: [gmx-users] g_msd for many molecules

Thanks for this Vitaly and Justin. George > The resulting MSD will correspond to the average from individual atoms. > > Calculating MSD of an individual atom and ascribing it to a [small] > molecule, which this atom belongs to, is reasonable. Assuming that > averaged > MSD from atoms correspond to