[gmx-users] g_sorient with -v23 option

Hi, all, I try to use g_sorient program to analyze SPC water molecules orientation around atomic ion. As I understand two molecule vectors are analyzed. For theta_1 calculation the dipole moment direction is used. Other two orthogonal vectors may be analyzed through theta_2 depending on -v23 op

Re: [gmx-users] Infrared

Hi, Hernan. You wrote 16 Jan 2012 ?., 19:23:27: > Dear gmx-user, > I am working in the dinamicas fo aluminophosphates material. I need to > calculated de IR spectrum from the trajectory. if is it possible to do > this with gromacs?, GROMACS is great! Couple years ago I calculated with gromacs

[gmx-users] force field for argon

Dear gmx'ers, Inspecting gromacs' OPLSAA files, I find here two atom types for argon. File ffoplsaa.atp includes: opls_097 39.94800 ; Argon from Verlet & Weis Mol.Phys.,24,1013 (1972) and Ar 39.948; Argon LJ parameters are (file ffoplsaanb.itp): [ atomtypes ] ; name bond_t

Re: [gmx-users] Re: Polarizable water model

Hi, Alex. You wrote 21 July 2011, 8:06:11: >>> Is any polarizable water models are available in ITP format? Or may be I >>> should prepare .itp from some articles? In recent mail archive I've found >>> some mentions about SWFLEX-AI model. Also I've found van der Spoel's >>> article. May be somebo

Re: [gmx-users] group temperatures and kinetic energies

I'm awfully sorry for groundless troubling! The sum of group kinetic energies IS STRONGLY EQUAL to the total one. Really I did compared the outputs of DIFFERENT simulations... > Dear gmx'ers, I am somewhat confused relating temperatures and kinetic energies in gromacs output. I simulate NVE sy

[gmx-users] group temperatures and kinetic energies

Dear gmx'ers, I am somewhat confused relating temperatures and kinetic energies in gromacs output. I simulate NVE system of N0 rigid molecules in vacuo, 'comm_mode' is set to 'None'. When I check the output 'Kinetic En.' and 'Temperature', the relation between them (see Eq. (3.13) of Manual) co

Re: [gmx-users] Radius of Gyration

Hi, C.. You wrote 1 ноября 2010 г., 22:09:36: > Does someone knows which equation is g_gyrate using to calculate the Rgx, Rgy, Rgz components of the Rg and which is the relation between them? I thougth that it was: Rg2=Rgx2+Rgy2+Rgz2, but at least for my results this is not the case. Sure,

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

[gmx-users] how to correct velocities in trajectory file

Dear gmx'ers, I've done a long NVE simulation in vacuo. During this run I had to take care to diminish the total energy drift, so my choice was comm_mode = None Now, analysing a smaller subsystem (solute + shell of solvent) I want to exclude its COM movement. Sorry, I fail to find any instruct

Re[2]: [gmx-users] 5 identical simulations --> 5 different results, why?

Hi, Justin. You wrote: > Ricardo O. S. Soares wrote: >> Hello dear users, >> in order to introduce Gromacs to a few students, I'm taking five >> computers with the same operational system (ubuntu), to run the same >> simulation independently. I prepared a box o water and ran all standard >> s

Re: [gmx-users] g_dipoles, average not the same as from g_analyze

Dear Emanuel, Please, check http://lists.gromacs.org/pipermail/gmx-users/2010-March/049316.html and Berk reply. I did never use -av (-a ?) option, maybe there is similar bug in average.xvg. Anyway last column of Mtot.xvg gives really correct norm of M_tot vector! Regards, Dmitri -

Re[6]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

nd consider submitting a bugzilla. Sure. > Cheers, > Tsjerk > On Wed, Jun 9, 2010 at 8:54 AM, Dmitri Dubov wrote: >> First, sorry for the revival of this thread so late (maybe it should be >> better to start a new one). >>> - Original Message - >>>

Re[4]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

First, sorry for the revival of this thread so late (maybe it should be better to start a new one). > - Original Message - > From: Dmitri Dubov > Date: Thursday, May 27, 2010 19:11 > Subject: Re[2]: [gmx-users] Non-conservation of total energy while > using structure fil

Re[2]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

Dear Mark, thank you for your prompt reply. > - Original Message - > From: Dmitri Dubov > Date: Thursday, May 27, 2010 15:41 > Subject: [gmx-users] Non-conservation of total energy while using > structure file to resume the simulation > To: Discussion list for GROMA

[gmx-users] Non-conservation of total energy while using structure file to resume the simulation

Dear GMX'ers! I simulate system of about hundreds of water molecules in NVE ensemble with md integrator. Every 100 ps I need to change slightly some parameters, say, electric field and to continue the simulation from this point. As I realize I cannot go on my run using the checkpointing and tpb

Re[2]: [gmx-users] how to get averaged coordinates for a residue in a time interval?

Hi all, One more similar question: How can I get (in the quickest way!) any form of the Lindemann parameter for rather big molecular crystal? (I mean averaged relative fluctuations in the intermolecular distance) > Well, you could also use g_rmsf with -b and -e, and a suitable index file... >

[gmx-users] huge field.xvg output

Dear GMX'ers, I'm watching electric field effect to small systems (~20 atoms). Simulations are rather long, about 200 ns, and the output is infrequent. Without electric fiels all is right. But when applying small field by the line in mdp-file: E-x = 1 0.1 0.1 my output includes huge (more than

[gmx-users] inaccuracy in g_dipoles log

Dear GMX'ers, Maybe it will be usefull for somebody: Struggling with the output of g_dipoles, I've found an inaccuracy in its log. Namely, line Total < |M| >^2 = 1.23456 Debye^2 means in fact Total |< M >|^2 = 1.23456 Debye^2 So the true < |M| > value cannot be obtained from this figure! R

Re[2]: [gmx-users] using SETTLE for constraints

rom a user point of view, this will not change much though, > since settle is only useful for water and a user (nearly) never > writes a topology for water. > Berk > Date: Mon, 7 Sep 2009 18:28:05 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re:

[gmx-users] using SETTLE for constraints

Dear GMX'ers, I am confused with some basic questions about using SETTLE constraining algorithm in gromacs. 1) This solution of SHAKE is used, particularly, for spc water. So spc.itp file contains the [ settles ] section, and there is no another [ constraints ] within it. But the parameter "c

Re[2]: [gmx-users] clustering dynamical structures

Mark wrote: > Dmitri Dubov wrote: >> Dear GMX'ers, >> Many gmx tools (g_rms, g_rmsdist, g_cluster etc.) calculate RMSD of >> distances. Take some molecule having two docking sites (A and B) and >> hydrated with two water molecules (C and D). Let's inspect t

[gmx-users] clustering dynamical structures

Dear GMX'ers, Many gmx tools (g_rms, g_rmsdist, g_cluster etc.) calculate RMSD of distances. Take some molecule having two docking sites (A and B) and hydrated with two water molecules (C and D). Let's inspect two structures realized. The first structure is with C docking to A and D to B, and t

Re[2]: [gmx-users] params for g_cluster and g_clustsize

Hi, Erik! Many thanks for your exhaustive reply. > Dmitri Dubov skrev: >> Thanks, David. >> Sorry, maybe my questions were too fuzzy. >> They concern the definition of cluster in these codes. >> 1) When we estimate through single linkage whether the structure &

[gmx-users] indexing largest cluster with g_clustsize

Dear gmx'ers! One more question on g_clustsize routine: It produces an index file with the atom numbers of largest cluster. But how it works in an evaporating system where the number of clustered molecules reduces greatly through the trajectory? What frame the maxclust.ndx file concerns to? --

Re[2]: [gmx-users] params for g_cluster and g_clustsize

(which is unusual for single linkage) relate to other algorithms for cluster partitioning. Is it right? Dmitri > Dmitri Dubov wrote: >> Dear gmx'ers, >> Could you explain me the following points in manuals for g_cluster and >> g_clustsize programs? >> 1) M

Re[2]: [gmx-users] params for g_cluster and g_clustsize

ngle linkage with default values) to the same system how different would be the cluster partitions? Thanks one more. Dmitri > Dmitri Dubov wrote: >> Dear gmx'ers, >> Could you explain me the following points in manuals for g_cluster and >> g_clustsize programs? >

[gmx-users] params for g_cluster and g_clustsize

Dear gmx'ers, Could you explain me the following points in manuals for g_cluster and g_clustsize programs? 1) Manual for g_cluster: "single linkage: add a structure to a cluster when its distance to any element of the cluster is less than cutoff... Other options... -cutoff real 0.1 RMSD cut-off

[gmx-users] MPI gromacs under cygwin

Hi, all! Is are any who uses GMX in MPI mode under cygwin? I'm trying to install it. Based on oldgromacs site and wiki I installed cygwin, FFTW and LAM/MPI. Unfortunately I failed to install libaio and leaved it out. But when configuring gromacs with ./configure --enable-mpi --disable-float --

[gmx-users] conversion to tip5p

Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar command for tip5p, the output

[gmx-users] Looking for polarizable and flexible water model

Dear gmx-users, For my simulations i'm looking for polarizable water model.  Shell models implemented in GMX are good-quality. But the question is that the model should be not only polarizable but also FLEXIBLE. To my present knowledge, there are only two alteratives. The first one is van Maar

[gmx-users] Ordering with trjorder

Dear gmx_users, could you clarify me how the "trjorder" procedure works? Manual says "For each frame of the trajectory the selected molecules will be reordered according to..." and so on. Does it mean that the ordering within each frame is INDEPENDENT on the prehistory and further moving of t

[gmx-users] mpi.h is missing...

Dear GMX users, Sorry for my stupid question, but unfortunately I'am very poor programmer... Earlier I have installed gromacs 3.3.3 under SUSE Linux 10.3 both in single and in double precision mode. Both versions work well. Now I try to add MPI version of mdrun (useful for my Dual Core Intel mac

Re: [gmx-users] Polarizative models for water

On Tue, 29 Apr 2008 16:49:24 +0200 David van der Spoel <[EMAIL PROTECTED]> wrote: Dmitri Dubov wrote: Dear David, Thanks for your short but instructive reply. Now I've start the simulation with your SW-model and see that it runs tenfold slower than analogues simulati

Re: [gmx-users] Polarizative models for water

uming, isn't it? How can I minimize the energy only at every Nth step? Sincerely, Dmitri --- On Mon, 28 Apr 2008 10:49:38 +0200 David van der Spoel <[EMAIL PROTECTED]> wrote: Dmitri Dubov wrote: (for David van der Spoel, imho) D

[gmx-users] Polarizative models for water

(for David van der Spoel, imho) Dear David, I am doing some similations of large water cluster with tip4p flexible model. I would like to include polarizability effect in the simulation, but trying it get twofold problem. First, I need the input gro-file with dummy and shell particles. I faile