RE: [gmx-users] g_rdf -surf

Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. However, the calculated RDF rises up to 41000 in long

RE: [gmx-users] g_rdf -surf

12 5:54 PM, Payman Pirzadeh wrote: Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. Ple

RE: [gmx-users] g_rdf -surf

...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: February-13-12 12:24 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] g_rdf -surf Hello, Thanks for your attention. A word was missing in my previous e-mail!! The g(r) is NOT normalized. Here was my command:

RE: [gmx-users] g_energy

Hello, I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen. Could you please clarify how it is calculated? In a system with a protein and water, what does it correspond to? Best, Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...

RE: [gmx-users] g_energy surf*surftens

Hello, In calculation of the surf*surftension with g_energy, does this quantity have any meaning when one deals with a protein in water(water fills up the box)? Can it be indicative of the surface tension of protein and water? Thanks. Paymon -- gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] selecting res CYS from G53a5 using pdb2gmx

Hi, I am using gromacs 4.5.4, and I am generating a topology file using G53a5 force field. My protein has a Cys residue which is supposed to be in thiolate state (negatively charged side chain). During issuing the pdb2gmx command I use the switch -inter to be prompted about the charge state of the

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

53a5 using pdb2gmx On 1/6/13 4:45 PM, Payman Pirzadeh wrote: > Hi, > I am using gromacs 4.5.4, and I am generating a topology file using > G53a5 force field. My protein has a Cys residue which is supposed to > be in thiolate state (negatively charged side chain). During issuing &

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: January-07-13 5:28 PM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx Dear Justin, I have been able to temporarily solve my force field parameter problem (at least test the new para

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

ary-07-13 5:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/7/13 7:36 PM, Payman Pirzadeh wrote: > Two clarifications: > 1. can utilization of an index file help during topology generation > for my problem? No. Reading pdb2gm

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

ng pdb2gmx On 1/8/13 1:37 AM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for your suggestions. It all made sense. > But I ran into a strange problem. I checked the mail list, and all I > found was about misspelling the force field name. I copied the whole > gromos53a5.ff directo

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 4:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:09 PM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for the tips. Things worked sm

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:09 PM, Payman Pirzadeh wrote: > Dear Justin, > Thanks for the tips. Things worked smoothly up to the point when I > wanted to run an actual simulation. When I wanted to run gro

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 6:58 PM, Payman Pirzadeh wrote: > Hi, > Found my solution; made an index file which had the prote

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

:25 PM, Payman Pirzadeh wrote: > I had modified three files: aminoacids.rtp, aminoacids.hdb and > residuetypes.dat. All these modifications were done prior running pdb2gmx. > So, I will be glad if you could let me know what the problem is. From that description, everything should be fine.

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

t, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/8/13 8:05 PM, Payman Pirz

Re: [gmx-users] changing protonation state of a residue during a simulation

Hello, I am simulating a protein using side chain pKa values estimated from PROPKA based on crystal structure of the protein. I re-estimated the pKa of side chains after running 10 independent replica of 50ns (500ns in total) of NPT simulations. It turned out that the average pKa of a surface Glu w

RE: [gmx-users] g_covar -ascii

Hello, I am interested in dynamical analysis of my protein. In the manual, it says -ascii generates a file that includes the whole covariance matrix, and -xpma writes the atomic covariance matrix per pair of atoms. I was wondering if there is a way to have this atomic covariaces in the .dat file wi

[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs

Hello, I am trying to generate a topology file for my protein which has three disulfide bonds using ffG53a5. I realized in the topology file that the force field parameters for bonds, angle and dihedrals of my S-S bonds are missing. I found the following thread about this issue: http://lists.grom

[gmx-users] restarting a crashed job

Hello, My simulation crashed in the middle and I used the "-cpi checkpoint.cpt -append" option to continue. However, GROMACS cannot continue and complains about not being able to open the corresponding .trr file. I checked my folder, the trr file is there and the name is the same as the *.tpr and

[gmx-users] itp and gro files

I was wondering if the order of sites in .gro file should be the same as in .itp file. Payman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.

RE: [gmx-users] itp and gro files

Thank you very much. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: May 6, 2009 8:25 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] itp and gro files Payman Pirzadeh wrote: >

RE: [gmx-users] Some molecules disconnected into many parts after EM

Hi Yanmei, I had this problem with water molecules, and I found that any time I changed the constrains without changing the boxes I generated through 'editconf'. So, after changing the constrains, I had to redo all my box generation process, then it was fine. But I ran into another problem and tha

[gmx-users] make install-mdrun

Hi All, I realized that I am missing (Lib and bin folders) analysis tools and mdrun MPI. I re-installed the GROMACS 4.0.3, and I found that when I get to 'make install-mdrun' the following messages show up ( I am just copying last lines): make[2]: *** [install-libLTLIBRARIES] Error 1 make[2]:

RE: [gmx-users] make install-mdrun

permissions in /usr/local/. So, configure gmx to be installed in your local dir. ./configure --prefix=/global/home/pirzadeh/gmx404 On May 8, 2009, at 10:10 AM, Payman Pirzadeh wrote: Hi All, I realized that I am missing (Lib and bin folders) analysis tools and mdrun MPI. I re-instal

RE: [gmx-users] make install-mdrun

-users] make install-mdrun Payman Pirzadeh wrote: > Thanks Diego, > > But, the latest I found on downloads of gromcs webpage was 4.0.3! Is > 4.0.4 somewhere else? The homepage and wiki both have the links to 4.0.4, or you can simply change the ftp link to point to gromacs-4.0.4 inst

[gmx-users] -np switch

Hello, When we use 'mdrun' or 'grompp' with the switch '-np' we specify the number of nodes according to the manual. Does it mean if the nodes have 2 processors, then the simulation will be run on 4 CPUs or in -np we should specify 4 instead of 2? Payman _

[gmx-users] gromacs on glacier.westgrid.ca

Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman _

RE: [gmx-users] gromacs on glacier.westgrid.ca

s, Tsjerk On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh wrote: > Hi All, > > Is there anyone who is running gromacs on glacier.westgrid.ca machine? If > yes, I will be appreciated if he/she can tell me how to run gmx on this > facility. I either get error messages which says

RE: [gmx-users] gromacs on glacier.westgrid.ca

g run at: `date`" ${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest echo "Job finished at: `date`" Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@grom

RE: [gmx-users] gromacs on glacier.westgrid.ca

aries. You also have make sure that you source the appropriate path to mdrun in your script and that your GMXLIB path is correctly set. Hope that helps, Nicolas Payman Pirzadeh a écrit : > Hi Justin, > Following is the script I use. But remember several points: > 1. I compiled the g

[gmx-users] gromacs on glacier

Hi, I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem still persists. But what I found is that it can be run on a node with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . it will crash. Following are the last lines reported in different files: "In the

[gmx-users] Energies in simulation

Hi, I am using my own water model which I developed its .itp file. When simulation is done after 1ns and energy is kinetic and potential energies are analyzed, the kinetic value is almost OK, but the potential energy is almost half of the value reported in literature and another MD code that I am

RE: [gmx-users] Energies in simulation

simulation Payman Pirzadeh wrote: > Hi, > > I am using my own water model which I developed its .itp file. When > simulation is done after 1ns and energy is kinetic and potential > energies are analyzed, the kinetic value is almost OK, but the potential > energy is almost

RE: [gmx-users] Energies in simulation

romacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:13 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: > To the best of my knowledge no, but how can I check that? > A. read the original paper: is your topology correct

RE: [gmx-users] gromacs on glacier

an -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Hi, > > I had the c

RE: [gmx-users] Energies in simulation

or GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: > Here is the content of .itp file which I developed: > > ; This is an itp file to describe water's six-site model by H. Nada and J.P. > J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401

RE: [gmx-users] gromacs on glacier

:56 AM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Hi Justin, > Since the manual itself was not sufficient, I asked some other people who > are running GROMACS in our group (but they run only on 2 CPUs). Here are the > steps I to

RE: [gmx-users] Energies in simulation

ginal Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: June 8, 2009 11:58 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energies in simulation Payman Pirzadeh wrote: > Well, when I set the box, I used &#

RE: [gmx-users] gromacs on glacier

emkul Sent: June 8, 2009 1:53 PM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Dear Justin, > Here is the mpich version: > MPICH Version: 1.2.7p1 > MPICH Release date: $Date: 2005/11/04 11:54:51$ > MPICH Patches ap

[gmx-users] making a box of water

Hello, I am trying to make a box of water from three different water models. I can make one from my own water model, but when I want to test TIP4P and SPCE, as soon as it comes to energy minimization step and using grompp, I get the following error message: Program grompp, VERSION 4.0.4 Sourc

RE: [gmx-users] making a box of water

users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 6:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hello, > > I am trying to make a box of water from three different water models. I > ca

RE: [gmx-users] making a box of water

emkul Sent: July 14, 2009 7:07 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water You need to #include an appropriate force field that contains the [defaults], [atomtypes], etc. before you can define a [moleculetype]. -Justin Payman Pirzadeh wrote: > Here is my .to

RE: [gmx-users] making a box of water

o: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Will #include "ffgmx.itp" solve my problem? Would it be a general solution > or in each case I should specify (if I add other solutes such as proteins)? > Well, ffgmx is dep

RE: [gmx-users] making a box of water

ayman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top fil

RE: [gmx-users] making a box of water

15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hi again, > I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in > the [atoms ]are specifies as opls_???, doesn't grompp check the

[gmx-users] Energy of a box of water

To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Thanks Justin. > Unfortunately, I realized that after I sent the e-mail. Anyways, I started > running to models: SPCE and TIP4P to check the energies of these systems to > figu

RE: [gmx-users] Energy of a box of water

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 2:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water Payman Pirzadeh wrote: > Hi, > I tested

RE: [gmx-users] Energy of a box of water

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 2:38 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water Payman Pirzadeh wrote: > -Origi

RE: [gmx-users] Energy of a box of water

PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy of a box of water Payman Pirzadeh wrote: > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of David van der Spoel > Sent: July 15, 20

[gmx-users] making a box of water

-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Thanks Justin. > Unfortunately, I realized that after I sent the e-mail. Anyways, I started > r

RE: [gmx-users] making a box of water

I forgot to mention, the dimensions of current simulation box are: 27.154A* 31.354A* 103.386A Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 7:24 PM To: 'Discussion list for GR

RE: [gmx-users] making a box of water

el > Sent: July 15, 2009 12:23 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] making a box of water > > Payman Pirzadeh wrote: >> Thanks Justin. >> Unfortunately, I realized that after I sent the e-mail. Anyways, I started >> running to models

RE: [gmx-users] making a box of water

: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > Hello, > Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the > rvdw cutoff to 10A, but problem was still there. > Now I made my box bigger by using a visualization

RE: [gmx-users] making a box of water

Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > But, I am using a .pdb file as the input of the gromacs. Does the > preparation of pdb file differ from software to software? > It shouldn't, and I'm not 100% sure on how Gromacs handles

[gmx-users] minimzation problem with a heterogeneous system

acs.org] On Behalf Of Mark Abraham Sent: July 16, 2009 12:39 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > You were right! The dimensions of the box are zero in the .gro file. Should > I change them to the values I have? Set th

RE: [gmx-users] minimzation problem with a heterogeneous system

romacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, July 16, 2009 8:40 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] minimzation problem with a heterogeneous system Payman Pirzadeh wrote: > Hello, > I have a configuration in which half of t

[gmx-users] reliability of NOTES

...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:38 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: > You were right! The dimensions of the box are zero in the .gro file. Should > I

[gmx-users] genconf

OK! Thanks for the tips on thermostat. I multiplied my .gro file by using the command "genconf". My original box has non-zero charge, but the generated bigger box has some charges: NOTE 2 [file sixsitemodel.top, line 8]: System has non-zero total charge: -1.220703e-04 Then, during minim

RE: [gmx-users] genconf

gmx-users] genconf Payman Pirzadeh wrote: > OK! Thanks for the tips on thermostat. > > I multiplied my .gro file by using the command "genconf". My original > box has non-zero charge, but the generated bigger box has some charges: > > Define "non-zero." Is

RE: [gmx-users] genconf

-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > In my previous e-mail, I posted the amount of charge given by GROMACS: > >

RE: [gmx-users] genconf

romacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 21, 2009 6:47 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > I am so sorry! I had sth in mind and I wrote sth else!!! > My original box has zero charges and GROM

RE: [gmx-users] genconf

list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > Yes and no! > Sometimes there is an overlap, but sometimes I could find nothing! In the > simplest case, how can we avoid overlaps in a way that the crystal structure > is maintained under pbc? > Can th

RE: [gmx-users] genconf

cs.org] On Behalf Of Payman Pirzadeh Sent: July 22, 2009 9:22 AM To: 'Discussion list for GROMACS users' Subject: RE: [gmx-users] genconf Thanks a lot Mark! I will run the system for equilibration and then try to replicate it. I will keep you guys posted. Payman -Original Message-

RE: [gmx-users] genconf

: July 22, 2009 6:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > Hello, > I minimized the initial output (from another simulation) first; then I > replicated it. This time, the minimization of the bigger box was done more > easily!

RE: [gmx-users] Re: wierd behavior of mdrun

There is sth strange about this problem which I suspect it might be due to the mdp file and input. I can run the energy minimization without any problems (I submit the job and it apparently works using the same submission script)! But as soon as I prepare the tpr file for MD run, then I run into th

RE: {Spam?} Re: [gmx-users] Re: wierd behavior of mdrun

> > On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote: >> Payman Pirzadeh wrote: >>> There is sth strange about this problem which I suspect it might be due to >>> the mdp file and input. I can run the energy minimization without any >>> problems (I submi

[gmx-users] a naive question on restraints and constraints

Hi, I read the wiki and manual on constraint and restraints, and I am still a bit confused. But, my question is, should I remove the restraints after equilibration in production phase? What about constraints? How should I know my system really needs either of them (is there a general rule or pr

[gmx-users] viscosity calculation

Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Regards, Payman

RE: [gmx-users] viscosity calculation

list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: > Hello, > > I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity > of my system which is water. Two files are generate: *.xvg and the > enecorr.xvg. Now, what

RE: [gmx-users] viscosity calculation

[mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: > Well, two questions: > > 1. My bulk values are fluctuati

RE: [gmx-users] viscosity calculation_2

Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: > Well, two questions: > > 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like > very weird

RE: [gmx-users] viscosity calculation_2

: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 2:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation_2 On 2010-09-29 22.00, Payman Pirzadeh wrote: > Adding to my previous comme

RE: [gmx-users] viscosity calculation_2

It does not explain for all files or all columns. For example, in the evisco.xvg, the following lines are written, but there are 5 columns (one of which is time). What are the rest? And the unit of the column (written below) is not clear to me. @title "Shear viscosity using Einstein relation"

[gmx-users] g_principal outputs

Hello, When we calculate the principal axes of protein, for each axis file, there are 4 columns. The first one is the time (ps), but there are no descriptions in the files about the rest. A little explanation will be very helpful. Regards, Payman -- gmx-users mailing listgmx-users@gr

RE: [gmx-users] editconf

After rotation, wouldn't a minimization with very very small steps solve the problem? Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:14 PM To: Discussion list for GROMACS users Subject

RE: [gmx-users] editconf

OMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 12:22 PM, Payman Pirzadeh wrote: > After rotation, wouldn't a minimization with very very small steps solve the > problem? Only if the solute surface was very close to being symmetric about the rotation axis. Since th

[gmx-users] viscosity calculations

Hello, I am trying to calculate the viscosity of my pure water system at 275K. The system has run for 40ns. I issued the following command: g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis sixsitewater_275K -b 0 -e 4 The numbers I get in the output file are

RE: [gmx-users]site-site radial distribution function

Hello, I have two questions about using g_rdf: 1. Is it meaningful to calculate the radial distribution of water molecules around a single atom of a surface residue, e.g. dangling OG1 oxygen of Threonine? (Does g_rdf takes care of the protein presence and the excluded volume?) 2.

RE: [gmx-users] trjcat xtc files

Your second guess is correct! I used grompp to restart (I had thought it might provide me with the chance to change things if needed). I was surprised initially when "cat" command did not work! The number of frames were most of the time less than what it should be. I also checked the 'trjcat -h'. I

[gmx-users] extracting individual particles properties

Hello, This is the third time I am sending this e-mail, and I am not sure why it does not show up on the list I have a simulation from which I have the .edr, .xtc and .trr files. I want to color my particles based on rmsd, potential energy, Sg (tetrahedral parameter) or any other parameters