Re: [gmx-users] K+ ions instead of NA+ for neutralization

Hi. I'm new to simulation and haven't tried that. Below is what I heard. Most of the time, the force field just treat K+ and Na+ as a sphere with charge and with no orbitals. So, K+ and Na+ ions in simulations are only different in radius (of the sphere). I guess it is ok to use K+ instead of

Re: [gmx-users] calculation of persistence length

Hi. I guess g_polystat can't do that. The online reference for gmx polystat (( http://manual.gromacs.org/programs/gmx-polystat.html) says: "...the persistence length is defined as number of bonds where the average cos reaches a value of 1/e." The number of bonds is one number. I don't think it

Re: [gmx-users] calculating total percentage of time from gibbs free energy landscape

can the following work? http://unix.stackexchange.com/questions/12068/how-to-measure-time-of-program-execution-and-store-that-inside-a-variable On Fri, Sep 11, 2015 at 7:57 AM, Naba wrote: > Is it possible to calculate total percentage of time invested to attain a >

Re: [gmx-users] reaction field and permittivity

thank you very much. On Thu, Sep 10, 2015 at 4:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/10/15 4:40 PM, Johnny Lu wrote: > >> Dear Users, >> >> I used mdp file at the following url for NVE vacuum simulation >> >> http://shourjya

[gmx-users] reaction field and permittivity

Dear Users, I used mdp file at the following url for NVE vacuum simulation http://shourjya.thinkbiosolution.com/wp-content/uploads/2013/02/nvevaccmdp1.txt Does epsilon_rf affect the simulation? epsilon_rf is dielectric constant beyond the cut-off. Since I set 0 for all the cut-off, the cut-off

Re: [gmx-users] Vacuum versus Water Simulation

After checking the motion of the whole molecule, the vacuum simulation has a stronger periodic component than the simulation in water. so it is fine now. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Vacuum versus Water Simulation

Dear Users, Hi. Alanine peptide was simulated in water and in vacuum under NVE ensemble. The magnitude of harmonic components were similar in both simulations (as shown by Fourier transformation). Is this normal? I thought without the damping by water, the vacuum simulation would have a much

[gmx-users] NVE Vacuum Fluctuation of Energy

Dear Users, I was trying to run NVE simulation of alanine peptide in vacuum with double precision gromacs 5.1. [plot of energy at http://postimg.org/image/6b6kksax7/] The total energy of the simulation still has fluctuation about 1kcal/mol. There should be no fluctuation of total energy in an

Re: [gmx-users] Split Trajectory file into parts

. On Mon, Aug 31, 2015 at 3:50 AM, Peter Kroon <p.c.kr...@rug.nl> wrote: > > > On 29/08/15 16:22, Justin Lemkul wrote: > > > > > > On 8/29/15 9:10 AM, Johnny Lu wrote: > >> Dear Users, > >> > >> Simulation writes to a Lustre file system (

Re: [gmx-users] charge neutralization in vacuum simulations

was that for mass spectrometry? On Tue, Sep 1, 2015 at 1:30 PM, Vitaly V. Chaban wrote: > To get a neutral protein, protonate all residues... > > Another question is what's your simulation goal, since protonated and > deprotonated residues behave obviously in a different

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Not sure if those are for 2-propanol as a liquid or interaction between 2-propanol and protein. from googling "2 propanol opls/aa" 1. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids The parameters are in the supporting

Re: [gmx-users] OPLS/AA parameters for 2-propanol

that was by google. I haven't parametrized forcefields. did they just put the pieces in http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work for 2-propanol? On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > Not sure if those are for 2

Re: [gmx-users] extend a simulation just with xtc file

can extend simulation if the number of steps were reached. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations That said, does extending the simulation avoid the problems that you found in the simulation? On Tue, Sep 1, 2015 at 11:54 PM, Johnny Lu <johnny.lu...@gmail.com>

Re: [gmx-users] Gromacs-5.1 XLC Seg. Fault.

what is the computer you are using? i tried to build gromacs 4.6.7 on IBM System p7 755. It was very tedious. I had to build cmake. I think I even tried to build gnu gcc compiler. The end result was that gromacs ran very slow. On Tue, Aug 25, 2015 at 4:08 PM, Carlos Aguni

Re: [gmx-users] extend a simulation just with xtc file

the position in xtc is not accurate enough for restarting simulation. xtc has no velocity. restart need position, velocity, and variables for the thermostat and barostat. Do you have any cpt file? may be you can run a restart using cpt and tpr files. On Mon, Aug 31, 2015 at 10:21 PM, Adriana

Re: [gmx-users] extend a simulation just with xtc file

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts On Tue, Sep 1, 2015 at 11:53 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > the position in xtc is not accurate enough for restarting simulation. xtc > has no velocity. > > restart need position, veloc

Re: [gmx-users] regarding box volume

I am new to simulation and haven't done any simulation for finding free energy. The following is my guess. How big are the molecules? If the box size is small then the concentration of the molecules is higher. May be the dissociation part is fine if: the hybrid can't see its mirror image (the

Re: [gmx-users] adding hydrogens to pdb file

Hi. reduce.exe seems not part of gromacs. http://kinemage.biochem.duke.edu/software/reduce.php On Thu, Aug 27, 2015 at 1:59 AM, elham tazikeh elham.tazi...@gmail.com wrote: Dear GMX users i want to *adding Hydrogens* to my lig.pdb (for making lig.itp file by ATB server) in cmd program in

[gmx-users] Split Trajectory file into parts

Dear Users, Simulation writes to a Lustre file system (a distributed file system made of many hard drives). About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it can't write the trajectory file. The file system still has lots of space. Not sure if that was because one of the many

[gmx-users] Restart -append

Dear Users, Simulation crashed. Gromacs 5.1 wrote last check point at about 4 min before the crash. Restart with mdrun -cpi (last check point file) -append Will the -append option get rid of the data for those 4 min between the last check point written and the crash? Thank you. -- Gromacs

Re: [gmx-users] How do I calculate the difference between two energy values?

Let x(t) be coulomb decoupling at time t. Let y(t) be VdW decoupling at time t. I guess the most safe way to get the answer is: calculate z(t) = x(t) + y(t) then, calculate standard deviation of z(t). If x(t) and y(t) are independent and both x(t) and y(t) are normally distributed, then I guess

[gmx-users] Thread, Multiple gpu, and sharing node

Dear Users, Hi. The system has about 3k atoms, and I used a rhombic dodecahedron box. The node in the cluster has 2 sockets and 12 cores per socket. (24 sockets in total) It also has 4 gpu. Will I waste cpu time, if I run with all 24 cores and assign 1 gpu to 3 cores? Should I compile for

[gmx-users] box size and neighbor list cut-off

Dear Users, Hi. Box vector length: 3.448, 3.448, 3.448 nm dodecahedron. (Box volume is 28.98 nm^3) Diameter of tripeptide: 1.248 nm Volume of tripeptide: 0.35503 nm^3 (from genbox output) Short range Neighbor list cut-off: 1.1 nm (set manually by rlist=1.1)

Re: [gmx-users] Respect waters in crystallographic pdb file?

I haven't tried that before. May be you can open the .gro files before and after genbox with a text editor. Then, check those water molecules? Those water molecules might have the same residue id. On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all,

Re: [gmx-users] box size and neighbor list cut-off

Sorry, I mean: If I use double precision gmx mdrun and constraint h-bonds, can I expect 1.135 rlist to give a drift in total energy as small as the one in the table? On Mon, Aug 17, 2015 at 5:07 PM, Johnny Lu johnny.lu...@gmail.com wrote: Thank you for the advices. I tried setting different

Re: [gmx-users] box size and neighbor list cut-off

Thank you for the advices. I tried setting different varlet buffer drift in the 1st equilibration run (nvt) for 5 seconds. From the log file of mdrun, I get: rlistverlet-buffer-drift 1.090.05 1.1140.005 1.1350.0005 = 1.1730.05 1.234

[gmx-users] refcoord-scaling without pressure coupling

Dear GMX users, If I set refcoord-scaling = com and also pcoupl = no, will that refcoord-scaling = com do anything (like introducing additional numerical error in a NVE simulation) ? Thank you. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] MD on protein-RNA complex

I guess: multi-chain means the system has multiple chains of polymer (such as peptide, or DNA/RNA). Some proteins have several peptide chains connected together. heterogeneous system: protein and RNA are different, and so protein + RNA is a heterogeneous system. Gromacs can simulate protein + RNA

[gmx-users] Test if Trajectories are Independent

Hi. Is there a good way to test if a set of trajectories are independent from each other? I was thinking about a) show that the initial structures of the trajectories are sufficiently different. b) calculate rmsd between corresponding frames of two trajectories. If the trajectories are

Re: [gmx-users] Element naming format in .pdb file

may be try both ways in a small file. feed it to pdb2gmx and then check the topol.top file to see if it uses the correct forcefield name? On Sat, Dec 20, 2014 at 12:12 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Dear all, I am trying to study wetting of Graphene oxide. I have prepared a

Re: [gmx-users] Ions drifting

If the Na or Cl ion don't strongly bind to the protein, as described by the force field, then they might not always bind to and stay with the protein in the simulation. If that is what you want, I guess you can artificially add a restraint to make the ion to stay closer to the protein ... I'm not

Re: [gmx-users] AMD GPUs

How about the open cl port of gromacs? http://streamcomputing.eu/blog/2014-11-01/ported-gromacs-cuda-opencl/ might have to check the list of bugs of 5.0 though. On Thu, Dec 18, 2014 at 5:16 AM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, Please don't hijack other discussion threads!

[gmx-users] compiling for xeon phi

Hi. How to compile double precision gromacs for xeon phi? (is that possible?) Do I need to use intel compiler, or gnu c/c++ is fine? Is the xeon phi code of gromacs 5.0.4 very different from the xeon phi code of gromacs 4.6.7? In the cmake command, do i have to change

Re: [gmx-users] CG MD Simulation of DNA and PAMAM dendrimers

Hi. This mail list can not take attachment. So it might be better to just past the mdp file in the message. At which time step did the segmentation fault happen? On Wed, Dec 17, 2014 at 1:43 PM, Doa Hawamdeh hawamdeh@gmail.com wrote: Dear GROMACS users: I want to study the complexation

Re: [gmx-users] Ions drifting

Hi. I guess the pbc option only make a previously non-periodic box become periodic. Do you want to: 1. Make the Na or Cl- ion always stay with the protein. Or 2. Make the protein looks like it stays at the center of the box. (but it can still rotate) I think the protein would look like it

Re: [gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed

Hmm. Did you try gcc? From the mail list, I heard that if the gnu c/c++ compiler is new enough, it builds faster gromacs than intel c/c++ compiler and mkl. I'm not sure about 5.0.4 though, and I am using 4.6.7 right now. On Tue, Dec 16, 2014 at 10:09 AM, Mike Hanby mha...@uab.edu wrote: Howdy,

[gmx-users] 0 +- 0.5 bar ok?

Hi. Are these pressures acceptable for reviewers? (I haven't submit anything to journals before). What would be different from a simulation with a truly 1 bar average pressure? System 1: NVT simulation gives an 0.0 +- 0.5 bar average pressure over 600ns with 2 fs timestep. When I averaged the

Re: [gmx-users] trjconv during transfer of .trr

Alternatively, is there a way to quickly check how many ns or frames do a .trr file contain? On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Before the queue manager of the cluster finishes transferring the .trr file to my homedirectory, if I start trjconv

Re: [gmx-users] trjconv during transfer of .trr

seems to be fine for slurm resource manager... so far. On Sun, Dec 14, 2014 at 5:50 PM, Johnny Lu johnny.lu...@gmail.com wrote: Alternatively, is there a way to quickly check how many ns or frames do a .trr file contain? On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu johnny.lu...@gmail.com wrote

Re: [gmx-users] Stop protein diffusion in simulation box to make a movie

hi. can this help? http://manual.gromacs.org/programs/gmx-trjconv.html On Sat, Dec 13, 2014 at 6:04 AM, Hassan Aaryapour hassan.grom...@gmail.com wrote: Dear Gromacs Users, I made a trajectory movie using VMD and smoothing increased for getting the residues motion slower, but the protein is

Re: [gmx-users] Need to Sort Out

Hi. I'm quite new to molecular dynamics too. How did you make that itp? Does your system contain only one protein/DNA molecule? May be try this tutorial for a single protein? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ Check multiple journal papers when you

[gmx-users] trjconv precision lost from double to single conversion

Hi. I'm using gromacs 4.6.7 If the trr trajectory file is from double precision calculation, and I use single precision trjconv to make a single precision trr trajectory, how much precision will I lose in position and in force? 1, 0.1, 0.01, or 0.001 angstrom and Newton? Is the lost of

Re: [gmx-users] trjconv precision lost from double to single conversion

. On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. I'm using gromacs 4.6.7 If the trr trajectory file is from double precision calculation, and I use single precision trjconv to make a single precision trr trajectory, how much precision will I lose in position

Re: [gmx-users] trjconv precision lost from double to single conversion

nevermind the 2nd question. it does reduce to about 1/10 size. On Fri, Dec 12, 2014 at 10:41 AM, Johnny Lu johnny.lu...@gmail.com wrote: When I test the disk space that I would save by getting rid the water in the trajectory, I found that only make the trajectory 1/4 as large as the original

[gmx-users] pmetune and restarting

Hi. I notice that after I stop a simulation by specifying the number of hours that it runs with -maxh, and then restarting the simulation, at the beginning of each restart, the pme is tuned again. Will that cause any error if I periodically restart the simulation? How big is the error? Is it

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

I'm not sure what happened, but so far when i install, i use full path instead of $(pwd) and it was fine for gromacs 4.6 and 5.0, 5.0.2. -- 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

[gmx-users] xeon-phi and double precision

Hi. Does xeon-phi make double precision gromacs faster? -- 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

Re: [gmx-users] Question on installation

May be just let gromacs build its own fftw3 library, by using -DGMX_BUILD_OWN_FFTW=ON in the cmake command, is a better idea? On Mon, Dec 8, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/14 12:38 PM, Igor Shchechkin wrote: Dear Gromacs users, I have obtained the error

Re: [gmx-users] Dihedral angle calculation in Gromacs

what do you mean by tensor? On Fri, Nov 28, 2014 at 4:22 AM, Ankit Agrawal aka...@gmail.com wrote: Hi I have pdb file which has crystal structure of Cadherin-23 (2WHV) with 2 domains EC1 EC2. So I want to calculate angle between two domains (tensor) along with the principal axes. regards

[gmx-users] Precision of xtc-precision

Hi. What is the exact precision of xtc-precision = 1000 ? Does that mean the positions are accurate to 0.001 nm, or to 0.1% ? I searched gromacs 4.6.7 manual and gromacs.org for xtc-precision, but didn't find answer. Thank you again. -- Gromacs Users mailing list * Please search the archive

[gmx-users] Different box volumes from gmxdump and g_energy

Hi. I get two different volumes with g_energy and gmxdump. Which one is true? For now, I'm trying to get a NVT simulation with correct pressure, after a 300 ns NPT equilibration. The 400 ns NPT equilibration has the following statistics, according to g_energy of gromacs 4.6.7, and the

Re: [gmx-users] Different box volumes from gmxdump and g_energy

, 0.0e+00} box[1]={ 0.0e+00, 7.50062e+00, 0.0e+00} box[2]={ 3.75032e+00, 3.75032e+00, 5.30375e+00} volume from box vector: 7.50062 * 7.50062 * 5.30375 = 298.385264414 On Wed, Dec 3, 2014 at 11:34 AM, Johnny Lu johnny.lu...@gmail.com wrote

Re: [gmx-users] Different box volumes from gmxdump and g_energy

. On Wed, Dec 3, 2014 at 1:04 PM, Mark Abraham mark.j.abra...@gmail.com wrote: A .cpt file has one frame in it. An .edr file has values and statistics from many frames. Are you comparing things that are comparable? Mark On Wed, Dec 3, 2014 at 6:56 PM, Johnny Lu johnny.lu...@gmail.com wrote

Re: [gmx-users] Different box volumes from gmxdump and g_energy

. Yet, the actual pressure of the NVT simulation is -1.40405 +- 0.39, and 0.4 bar is not within two standard deviations of this value. On Wed, Dec 3, 2014 at 1:08 PM, Johnny Lu johnny.lu...@gmail.com wrote: yes. I get an xvg file from the edr file with g_energy. Then from the xvg file, i

[gmx-users] dump current rlist in cpt

Hi. is it possible to check current rlist, and vdw cut-off in a cpt file. I want to know if the big energy jump upon extending/continuing/restarting simulation with gromacs 4.6.7 is caused by the load balancing bug ( http://redmine.gromacs.org/issues/1603) Thank you. -- Gromacs Users mailing

Re: [gmx-users] changing ewald_rtol

Thank you very much for the answer. On Tue, Nov 18, 2014 at 2:03 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Nov 18, 2014 at 7:38 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. from online manual: *ewald-rtol (1e-5)* The relative strength of the Ewald-shifted direct

Re: [gmx-users] Equilibration from Non-shifted to Shifted Potential

, given that the forces are not computed from the energies (e.g. by central difference or some such), what role does the potential energy play in the integration scheme? :-) Mark On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. If I change my potential from non

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

This seems to have nothing to do with shifted potentials or gpu. I run a tripeptide double precisiion NVE simulation on a machine with xeon cpu and without gpu. kill it, then continue it with the cpt file generated. That energy jump still exists. On Tue, Nov 11, 2014 at 1:39 PM, Johnny Lu

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing from a NPT

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

56 56 56, coulomb cutoff 1.350 DD step 4999 load imb.: force 41.0% On Tue, Nov 11, 2014 at 9:44 AM, Johnny Lu johnny.lu...@gmail.com wrote: by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum On Tue, Nov 11, 2014

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

uploaded the files at http://redmine.gromacs.org/issues/1640 On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing

[gmx-users] Avg. Volume in NPT by Small Coupling Time

Hi. How to get an accurate average volume for a system, such that the pressure will be at 1 bar in a subsequent NVT run using this average volume? Is it ok to use Berendsen barostat with a very small time constant (0.2 ps) ? (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2

Re: [gmx-users] Pressure Question

and velocity distributions (unlike Berendsen). I'd give serious consideration to rejecting a paper that used Gromacs and the Berendsen thermostat, particularly if they did not discuss why the known defects of Berendsen were acceptable for their work. Mark On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu

Re: [gmx-users] Avg. Volume in NPT by Small Coupling Time

mark.j.abra...@gmail.com wrote: Hi, I think that's fine for rapidly forcing the volume to be close to the right equilibrium value, with low fluctuations. Then switch to gentler NPT (or constant-volume) for making a proper observation of the pressure. Mark On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu

Re: [gmx-users] Pressure Question

If the problem of using a 11 bar simulation is as big as the problem of drawing conclusion from a single simulation, I guess I have to get a pressure closer to 1 bar. Thanks. On Thu, Nov 6, 2014 at 10:55 AM, Johnny Lu johnny.lu...@gmail.com wrote: I see. I'm using the V-rescaling thermostat

Re: [gmx-users] Version problem

can look for all files with name mdrun by $ find / -name mdrun * mdrun_search and then $ cat mdrun_search On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi, 'which mdrun' only tells you the location of the mdrun you're currently using and is no good here.

Re: [gmx-users] Version problem

I typed an extra space that shouldn't be there. $ find / -name mdrun* mdrun_search On Thu, Nov 6, 2014 at 5:03 PM, Johnny Lu johnny.lu...@gmail.com wrote: can look for all files with name mdrun by $ find / -name mdrun * mdrun_search and then $ cat mdrun_search On Thu, Nov 6, 2014 at 7

[gmx-users] speed of 5.0.2 v.s 4.6

Hi. Do the two version of gromacs with mixed precision have similar speed? Thanks again. -- 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 *

Re: [gmx-users] speed of 5.0.2 v.s 4.6

Thanks. I guess I will keep version 4.6.7 for now. On Wed, Nov 5, 2014 at 11:40 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes, in general. Mark On Wed, Nov 5, 2014 at 5:11 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Do the two version of gromacs with mixed precision have

Re: [gmx-users] Pressure Question

hard to say. You'd need to do multiple converged simulations at each set of conditions to know. First, make sure you've made a significant observation of the pressure. Mark On Tue, Nov 4, 2014 at 6:00 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. If my NVT simulation of a protein

Re: [gmx-users] Pressure Question

the protein has about 170 amino acid. On Wed, Nov 5, 2014 at 1:13 PM, Johnny Lu johnny.lu...@gmail.com wrote: The statistics was calculated for 80 ns of NVT simulation, after a 80 ns NPT simulation. In papers, I saw people talked about using the average volume of a previous NPT simulation

Re: [gmx-users] Pressure Question

(deviation from 1 bar) is acceptable. On Wed, Nov 5, 2014 at 2:35 PM, Téletchéa Stéphane stephane.teletc...@univ-nantes.fr wrote: Le 04/11/2014 18:00, Johnny Lu a écrit : Hi. If my NVT simulation of a protein in 30k molecules of water has a pressure of 11 bar (error 0.5 bar from g_energy

Re: [gmx-users] pseudo-random algorithm

29, 2014 at 6:23 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Before I start to feel optimistic about my alanine tripeptide simulation, can I know which pseudo-random number algorithm does my installation of gromacs 4.6.6 use? It was installed on linux centos 5 with kernel

[gmx-users] Pressure Question

Hi. If my NVT simulation of a protein in 30k molecules of water has a pressure of 11 bar (error 0.5 bar from g_energy), will the dynamics (not distribution of conformations) change enough that the mechanism inferred from this simulation be significantly more unreliable than the mechanism inferred

Re: [gmx-users] problems with testing a new gromacs installation (myfirst) for correctness

Hi. did you try to download the regression tests manually? I don't know if the problem that I encountered was the same one: http://comments.gmane.org/gmane.science.biology.gromacs.user/71882 I had to turn regression test download off in addition to setting path to regression test. On Sat, Nov

Re: [gmx-users] pressure dependence on volume.

One less thing to worry about then. I will try to fix this in another way. Thanks. -- 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

Re: [gmx-users] pressure dependence on volume.

, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Johnny, The density is M/V. The only parameter changing with pressure coupling is V, so the density and volume are fully correlated. No surprise there. Cheers, Tsjerk On Oct 19, 2014 2:27 AM, Johnny Lu johnny.lu...@gmail.com wrote: The frames

Re: [gmx-users] pressure dependence on volume.

. Is it so? Or manually setting the volume makes some magical differences? On Sun, Oct 19, 2014 at 10:24 AM, Johnny Lu johnny.lu...@gmail.com wrote: Thanks for answering my questions too. On Sun, Oct 19, 2014 at 10:18 AM, Johnny Lu johnny.lu...@gmail.com wrote: The averaged volume of the 1bar

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

how long were those simulations? Were there enough time for the new ensemble to equilibrate, if you changed ensemble from NVE to NVT? On Sun, Oct 19, 2014 at 11:34 AM, Wade wad...@foxmail.com wrote: Dear Mark and Lu, Thank you very much for your responses. Based on your suggestions, I

Re: [gmx-users] pressure dependence on volume.

Was the density calculated by # particles / volume ? If so, using volume (as I did), and using density would give the same wrong pressure, upon transitioning from NPT to NVT. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] pressure dependence on volume.

my bad. that formula for density is wrong. But I till don't see why using the same averaged density (instead of volume) for the NVT and NPT simulations would give a different result. On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com wrote: Was the density calculated

Re: [gmx-users] pressure dependence on volume.

Would manually setting the box size make vacuum bubbles? On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu johnny.lu...@gmail.com wrote: my bad. that formula for density is wrong. But I till don't see why using the same averaged density (instead of volume) for the NVT and NPT simulations would give

[gmx-users] Check for Vacuum Bubbles Density

Hi. The NPT simulation has 9K TIP3P water with 173 amino acid residues and uses Amber99SB-ILDN force field, and use Berendsen barostat and V-rescale thermostat. I plan to run NVT with the same pressure an temperature after this. The average density is 1015 kg/m^3 over 35ns. The density was near

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

For V-rescale thermostat, the bussi paper seems to say the tilde H is the integral of the auxiliary dynamics. Not sure if this is same as the conserved energy in gromacs, which is also the integral of the auxiliary dynamics. I guess numerical error causes the system to lose/gain total energy in a

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Oh, integrating with rectangles under the curve causes error. I guess larger time-steps can cause error in tilde H by this method of integration alone. On Sat, Oct 18, 2014 at 11:25 AM, Johnny Lu johnny.lu...@gmail.com wrote: For V-rescale thermostat, the bussi paper seems to say the tilde H

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Does double precision cause a less drop/rise in tilde H over time, when compared to a mixed precision run under same condition ? On Sat, Oct 18, 2014 at 11:28 AM, Johnny Lu johnny.lu...@gmail.com wrote: Oh, integrating with rectangles under the curve causes error. I guess larger time-steps can

Re: [gmx-users] Use NVT to mimic NVE

, Johnny Lu johnny.lu...@gmail.com wrote: The simulation get worse in a new way. I see that thermostat scales velocity and may not fix numerical error in potential energy. On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu johnny.lu...@gmail.com wrote: I just want something

Re: [gmx-users] Use NVT to mimic NVE

I mean here seems to say conserved energy is tilde H [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html ] On Sat, Oct 18, 2014 at 6:44 PM, Johnny Lu johnny.lu...@gmail.com wrote: The conserved energy from g_energy, which I saw someone say is tilde H, drop

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Does this old maillist post say tilde H is conserved energy? [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html ] On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Oct 18, 2014 at 4:32 PM, Wade wad...@foxmail.com wrote:

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

post at [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html ] On Sat, Oct 18, 2014 at 6:51 PM, Johnny Lu johnny.lu...@gmail.com wrote: Does this old maillist post say tilde H is conserved energy? [ https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

. On Sat, Oct 18, 2014 at 6:58 PM, Johnny Lu johnny.lu...@gmail.com wrote: Figure 2 of the Bussi paper has a diagram with constant tilde H for NVT simulation with 2fs time step, and another one with rising tilde H for NVT simulation with 40fs timestep, and say: for tilde H in the NVT calculation. We

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

, Oct 18, 2014 at 7:02 PM, Johnny Lu johnny.lu...@gmail.com wrote: The bussi paper is at [ marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf http://marge.uochb.cas.cz/%7Eroesel/teach/Clanky/paper5_Bussi_v_rescale.pdf ]. I seem to vaguely remember someone wrote if tilde H drop

Re: [gmx-users] pressure dependence on volume.

I searched the energy file made by g_energy, and found that NPT frames with very similar densities have very similar volume. So, I guess using density is same as using volume in this case. On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu johnny.lu...@gmail.com wrote: Would manually setting the box

Re: [gmx-users] pressure dependence on volume.

The frames with density closest to the average density also have volumes closest to the averaged volume. On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu johnny.lu...@gmail.com wrote: I searched the energy file made by g_energy, and found that NPT frames with very similar densities have very similar

Re: [gmx-users] Not achieving any speedup using Open MPI

i heard that mixing mpi and open mp together is bad idea (run more slow), unless the simulation has large number of atoms, and use many cpu. May be comparing gromacs running on a single computer, with and without openmp will show a difference in speed. On Fri, Oct 17, 2014 at 10:05 AM, Da-Wei Li

[gmx-users] pressure dependence on volume.

Hi. Mainly TIP3P water, 300K. The pressure is near 1 bar. A less than 1% error in volume would cause how much error in average pressure? From three npt simulations of 72 ns with Berendsen barostat, I get the average volume is 298.5 nm^3. Continuing from a frame with volume very close to 298.5

Re: [gmx-users] pressure dependence on volume.

At least for real water, a 0.2% error in volume can mean the pressure is ~30 bar when the target pressure is 1 bar. http://docs.engineeringtoolbox.com/documents/309/water-density-temperature-pressure_2.png On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. Mainly

Re: [gmx-users] pressure dependence on volume.

if the NVT simulations continuing from those frames would give me the 1 bar pressure. On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/17/14 11:49 AM, Johnny Lu wrote: At least for real water, a 0.2% error in volume can mean the pressure is ~30 bar when the target

Re: [gmx-users] Understanding comments in pdb2gmx output

Does the pdb file have alternative conformations for some side chains or atoms? Like a side chain may have 50% chance to be rotated left, and 50% chance to be rotated right. The crystallographer recognized these two possibilities, and give each possibility a 0.5 occupancy. It may look like LYSA

Re: [gmx-users] How to add iron parameter?

Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in pure md is not directional, as it should be. can molecular dynamics (md) simulate heavy metals, like iron, which have d oribtals? I heard that even calcium is a bit troublesome in md. On Wed, Oct 15, 2014 at 1:22 PM,

  1   2   >