Re: [gmx-users] Shift function: rcoulomb-switch

On 19/02/2012 2:01 AM, Juliette N. wrote: Hi, I am trying to figure out the best setting for cut offs and r_switch for my system based on shift functions. coulombtype = Shift vdw-type= Shift rcoulomb-switch = 1 rvdw-switch = 1 ; Cut-offs

Re: [gmx-users] a question about force fields

ark Best regards. Banafsheh On Sat, Feb 18, 2012 at 5:11 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 18/02/2012 7:23 PM, Banafsheh Mehrazma wrote: Dear all; I am wondering if the amber99 in gromacs package is the same as PARM99 in A

Re: [gmx-users] Regarding DispCorr

On 19/02/2012 11:21 PM, bipin singh wrote: Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. What does it do? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arch

Re: [gmx-users] Regarding DispCorr

s out some conditions for its use. It is likely from the nature of EM that it doesn't matter either way. Mark On Sun, Feb 19, 2012 at 20:20, Mark Abraham wrote: On 19/02/2012 11:21 PM, bipin singh wrote: Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres dur

Re: [gmx-users] Using CHARMM force fields in Gromacs, pt. 2

On 20/02/2012 4:56 PM, Jernej Zidar wrote: Hi. Several months ago I was asking how to import and use two CHARMM forcefields in Gromacs at the same time in MD simulations. The two forcefields are CGENFF and CHARMM36. I was able to add the polymer monomers and relevant parameters so I can n

Re: [gmx-users] Regarding DispCorr

) fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes emtol=100.0 emstep=0.01 pbc=xyz On Mon, Feb 20, 2012 at 05:03, Mark Abraham wrote: On 20/02/2012 2:23 AM, bipin singh wrote: Hello, Thanks for reply. As given in the manual, If we

Re: [gmx-users] double and single precision

On 20/02/2012 7:19 PM, Edvin Erdtman wrote: Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the doub

Re: Sv: Re: [gmx-users] double and single precision

On 20/02/2012 7:29 PM, Edvin Erdtman wrote: Hi So the best I can do now is to recreate the first part, and rerun "new" the simulations? If you have a full frame (positions+velocities+maybe energies, or a checkpoint file) then I expect so. Save your crossbreed files in case someone has a bet

Re: Sv: Re: [gmx-users] double and single precision

On 20/02/2012 9:13 PM, Edvin Erdtman wrote: Hi again How do I "set the env.var. GMX_ENX_NO_FATAL"? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. http://en.wikipedia.org/wiki/Environment_variable#Getting_and_setting_environment_variables Mark

Re: [gmx-users] water radial distribution function

On 20/02/2012 10:40 PM, Nidhi Katyal wrote: Dear all, I would like to plot g(OO) water radial distribution function.How should i use g_rdf or any other command to do this?Please help. Please read g_rdf -h, try things out and ask a focussed question. :-) Mark -- gmx-users mailing listgmx-u

Re: [gmx-users] Molecular Dynamics basics...

On 21/02/2012 12:11 AM, prashant kurkute wrote: Hi GROMACS users, I am a very novice to GROMACS.. .. My question may be very simple but very important to me..!!! These may be very basics... 1. What is the meaning of comm_mode and nstcomm.. I read the manual but

Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

On 21/02/2012 4:36 AM, Lara Bunte wrote: Hello I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types. In gromacs I have to put this para

Re: [gmx-users] Scaling/performance on Gromacs 4

On 21/02/2012 8:11 AM, Floris Buelens wrote: Poor scaling with MPI on many-core machines can also be due uneven job distributions across cores or jobs being wastefully swapped between cores. You might be able to fix this with some esoteric configuration options of mpirun (--bind-to-core worked

Re: [gmx-users] T-coupling problem?

On 21/02/2012 8:39 AM, Talal Alotaibi wrote: Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do "grompp", it gives me this error: A more sound protocol for preparation for MD probably involves

Re: [gmx-users] Interchain Disulfide Bond

On 21/02/2012 6:20 AM, jneeraj wrote: Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that

Re: [gmx-users] Re: Interchain Disulfide Bond

On 21/02/2012 12:33 PM, jneeraj wrote: Thank you Mark for you prompt response. I tried: $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f -o -p $grompp -f -c -p -o and it works perfectly, i.e. it correctly creates interchain disulfide bond. However, when I use charmm27

Re: [gmx-users] interface

On 22/02/2012 3:11 AM, mohammad agha wrote: Dear Gromacs Specialists, I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept the /x-/ and /y-/dimensions fixed, and double the system size in /z

Re: [gmx-users] Distance Restraints on Protein - possible at all?

On 22/02/2012 11:17 AM, NG HUI WEN wrote: *From:*NG HUI WEN *Sent:* Sunday, February 19, 2012 1:19 PM *To:* gmx-users@gromacs.org *Subject:* Distance Restraints on Protein - possible at all? Dear gmxusers, I have been trying to apply distance restraints on my protein but have been unsuccessfu

Re: [gmx-users] interface

ou need to find parameters for such a model. Then it's the same kind of approach as a mixed-solvent system (see gromacs webpage), only here it will be mixed fluid. Mark Best Regards Sara ---- *From:* Mark Abraham *

Re: [gmx-users] Adding new residue to the the force field

On 23/02/2012 6:02 AM, ramesh cheerla wrote: Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new atom types i added these atom types to the atomtypes.atp file and ffnonbonded.itp and I am using Buc

Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

On 23/02/2012 10:26 AM, Jose Borreguero wrote: Dear GROMACS users, While simulating a DLPC membrane, I noticed that it tends to diffuse along the normal (Z-axis) component. Is there a 'standard' restrain that is used to prevent such diffusion? The first option I thought was to restrain the ce

Re: [gmx-users] Fwd: how to add close proteins

On 23/02/2012 5:46 PM, rama david wrote: Hi GROMACS users, I wish to study proteins behaviour,With the help of command genbox -ci protein.gro -nmol .. -box -o -pI am putting the four peptide at random positions, but I need to put theem close enough so they are forming at least one hydrog

Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

membrane at Z=0.0 You can't have the bilayer drift unless the water drifts with it or through it. The former is more likely, thus you likely have COM motion. Mark -Jose On Wed, Feb 22, 2012 at 9:04 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 23/02/2012

Re: [gmx-users] rc or rlist in minimum image convention?

On 24/02/2012 10:55 AM, Juliette N. wrote: Hi all, My average size is 2.9 nm obtained from NPT under large pressure and now I intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about violating minimum image convention. That probably violates the parametrization of your for

Re: [gmx-users] Positive Coul. recip. term

On 24/02/2012 7:35 AM, Denny Frost wrote: Dear all, I am trying to equilibrate a solvent of pure ionic liquid. The system keeps exploding (after 2-5 ns) and I am not sure why, though I believe coulombic interactions are to blame. This is because the Coul-SR term is negative, but the Coul. re

Re: [gmx-users] rc or rlist in minimum image convention?

On 24/02/12, "Juliette N." wrote: > > > > On 23 February 2012 20:07, Mark Abraham wrote: > > > > > > > > On 24/02/2012 10:55 AM, Juliette N. wrote: > > > > > Hi all, > > > > > > My average size is 2.9 nm ob

Re: [gmx-users] tabulate potential

On 24/02/12, smith bill wrote: > > i need to add several customized potential functions into gromacs by > tabulating the potential. > However i have a question about tabulating: > How many customized potential functions can i add using tabulating? > > See manual 6.7.2 Mark -- gmx-

Re: [gmx-users] Options for the buckingham potential

On 24/02/2012 4:06 PM, ramesh cheerla wrote: Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-

Re: [gmx-users] Options for the buckingham potential

On 24/02/2012 5:15 PM, Mark Abraham wrote: On 24/02/2012 4:06 PM, ramesh cheerla wrote: Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp

Re: [gmx-users] Adding new residue to the the force field

2 at 7:32 AM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 23/02/2012 6:02 AM, ramesh cheerla wrote: Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new

Re: [gmx-users] Re: Internal water in the membrane receptor

On 24/02/2012 6:31 PM, James Starlight wrote: Up! :) Please provide me with the best sollution of my problem! I just want to copy some water mollecules from X-ray structure to my model and place it in the identical possitions inside the TM budle of my protein. What are the most trivial way t

Re: [gmx-users] Re: Internal water in the membrane receptor

than I'll minimise this editted structure to relax side chains of the residues wich are in contact with the new waters Might this aproach be usefull? Commonly I use it to prepare protein-ligand complexes. Might work, but there are lots of steric issues and potential problems. Mark James

Re: [gmx-users] li lin wants to share a link | Gromacs

On 24/02/2012 7:05 PM, ros...@kth.se wrote: li lin wants to a share a link on the Gromacs wiki: http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search li lin says: Dear all, Recently I made some tests, and I want to get same potential with the following method. (gmx 4.0.5.) F

Re: [gmx-users] Domain decomposition problems

On 25/02/2012 4:52 AM, Olivia Waring wrote: Dear Gromacs users, Could someone please shed light on the following problem? My system consists of an alkanethiol SAM (in the xy plane) with a layer of water on top. The mdrun command works when the box vectors are 1.1, 1.3, and 2.5, but the SAM fl

Re: [gmx-users] Adding new residue to the the force field

params ] . if it is mandatory to use pair types how can i get these values for this directive. You'll have to do some detective work starting at line 862. Mark Thanks in advance. On Fri, Feb 24, 2012 at 12:15 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 24/0

Re: [gmx-users] Re: Internal water in the membrane receptor

On 25/02/2012 5:37 AM, James Starlight wrote: Mark, So as I understood the ussage of X-ray structure as the starting model where the internal water is already present might be good in case to avoid those sterric issues doesn't it ? Yes. This was one of the options I suggested earlier. Wh

Re: [gmx-users] rerun problem

On 25/02/2012 9:07 PM, ahmet yıldırım wrote: Dear users, I am using Gromacs 4.5.4. I rerun the simulation using the following command: mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append Unfortunately remaining output didnt append to existing files (protein-RUN.xtc, protein-RUN.edr, protein

Re: [gmx-users] Re: gmx-users Digest, Vol 94, Issue 159

On 25/02/2012 6:45 PM, priya thiyagarajan wrote: hello sir, Thanks for your kind reply.. one small doubt sir.. its enough to give*mdrun -s md.tpr -cpi state.cpt * so that it ll automatically append my new data to the respective file .. Only if you are happy with the default filenames. Mark

Re: [gmx-users] gromacs: pdb2gmx error

On 25/02/2012 6:30 PM, venkatesh s wrote: Hi i got that error in the step of pdb2gmx what can i do i read also http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database can any one tell exact reason and how i handle further The exact reason is

Re: [gmx-users] gromacs: pdb2gmx error

On 26/02/2012 3:13 PM, venkatesh s wrote: Thanking you Mark Abraham for your valuable suggestion Here i used DNA Ligand Complex only is that any specific options is there? Please consider the advice here http://www.gromacs.org/Support about the kind of content that requests for help should

Re: [gmx-users] error

On 26/02/2012 3:58 PM, dina dusti wrote: Dear Gromacs Specialists, My total time for simulation is 60 ps (600 ns) because I work with MARTINI coarse-grained force field and this time is enough for my system, Different observables converge over different time scales. The autocorrelation t

Re: [gmx-users] error

On 26/02/2012 5:43 PM, dina dusti wrote: Dear Mark, Thank you very much from your response. Can you tell me what is the best solution for this warning, Please? No, I can't. Even if I wanted to (and I don't, because making decisions is your job), you aren't providing enough relevant informatio

Re: [gmx-users] how to set up pressure in gmx?

On 26/02/2012 8:36 PM, zhongjin wrote: Hello to all users, I am not sure how to set pressure if pcoupltype = semiisotropic it should be : ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic nstpcouple = -1 ; Time constant (ps

Re: [gmx-users] Residue 'HO4' not found in residue topology database

On 26/02/2012 10:08 PM, shilpa yadahalli wrote: Dear gmx-users, I am using CHARMM27 all-atom force field (with CMAP) - version 2.0 force field with gromacs 4.5.2 version. I want to retain my crystal waters in pdb file. I wrote crystal water according to the same convention when gromacs solvat

Re: [gmx-users]mdrun using old version

On 26/02/2012 10:42 PM, nicolas prudhomme wrote: Hi gmx-users, I don't know why, but my mdrun suddenly started to use the 4.0.7 version while I have installed only the 4.5.4 version. I have reinstalled gromacs 4.5.4 but when I run mdrun it still want to use the 4.0.7 version and can not read

Re: [gmx-users] Re: Internal water in the membrane receptor

On 27/02/2012 5:03 PM, James Starlight wrote: Justin, 2012/2/25 Justin A. Lemkul mailto:jalem...@vt.edu>> You likely have a [settles] directive applied the the XW molecules (crystal waters, yes?) and SOL. You can't do that. The block of molecules to which [settles] are applied

Re: [gmx-users] tau-p value

On 27/02/2012 6:35 PM, zhongjin wrote: Dear GMX users, I find that tau_p value is very important to NTP simulation, when I use tau_p = 1ps, the default value, the box change a lot, only when I use tau_p = 10 ps, it is OK. ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoup

Re: [gmx-users] Re: Internal water in the membrane receptor

On 27/02/2012 8:35 PM, James Starlight wrote: Mark, I've found a possible sollution to restrict oxygens of my X-ray water by possible plasing the below string in the TOPOLOGY.top of my system ; Include X-ray water topology #include "XW.itp" ; Include Position restraint file #ifdef POSRES_XW

Re: [gmx-users] cutting a cylinder from simulation box

On 28/02/2012 10:49 AM, Sanku M wrote: Hi, I have run a simulation of a fixed object in water using gromacs. Now, I want to analyze only water molecules which are present within a cylinder of certain radius (smaller than simulation box dimension in XY plane). I wonder whether gromacs has any

Re: [gmx-users] mdrun extension and concatenation

On 28/02/2012 3:50 PM, priya thiyagarajan wrote: hello sir, while performing simulation for 30ns, because of queue time limit my run terminated at 11.6ns.. then i extended my simulation using mdrun as you suggest.. while doing so i got error as Fatal error: Failed to lock: md20.log. Functio

Re: [gmx-users] query reg.

On 28/02/2012 3:36 PM, Vishwambhar Bhandare wrote: Hello, Is it possible to analyse structure during running simulation? Hw we can do that Make a copy of the trajectory file and then do whatever you want. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

Re: [gmx-users] How to calculate Cosine content of a trajectory?

On 28/02/12, a a wrote: > > > > > > > > > > > > > > > Dear Gromacs experts, > > > How to calculate the cosine content of a trajectory? > > > Best regards, > > > Catherine > > > > > Please start by looking in the manual. Mark -- gmx-users mailing listgmx-user

Re: [gmx-users] How to read AMBER's mdcrd files with GROMACS?

On 28/02/12, a a wrote: > > > > > > > > > > > > Dear Gromacs experts, > > > How to read AMBER's mdcrd files with GROMACS? Many thanks again for your > help. > > > > > Please see http://www.gromacs.org/Documentation/How-tos/Using_VMD_plugins_to_read_trajectory_formats_not_

Re: [gmx-users] A theoretical question

On 28/02/12, "Du Jiangfeng (BIOCH)" wrote: > Dear GMX-users, > > In my impression, a conventional simulation should be composed by: assemble > system --> energy minimization --> NVT and NPT equilibration --> MD > simulation, right? Now assume this procedure is correct, how about if there

Re: [gmx-users] adding a new residue type

On 28/02/12, Banafsheh Mehrazma wrote: > > Dear all; > I have used a modified guanine in my simulation before, with new parameters > added in amber99 force field and there was no error through the whole > simulation. now I'm trying to do a simulation with modified Guanine on a > differe

Re: [gmx-users] RE: A theoretical question

On 28/02/12, "Kukol, Andreas" wrote: > Hello, > > Firstly, proper equilibration is a technical requirement. The production MD > simulation might crash, if the system was not properly equilibrated. > > Secondly, if you want to study the properties of a macromolecule in solvent, > you must

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

On 29/02/2012 1:11 AM, lina wrote: On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann wrote: Thank you Vedat! Why do you use -DFLEXIBLE in md and in em? Why dont you use constraint algorithm (LINCS) in your simulation? Otherwise, the system is easily explode with lots of LINCS warning. That

Re: [gmx-users] change simulation temperature

On 29/02/12, "bo.shuang" wrote: > Hi, all, > > I have a question about change the temperature in simulation. When I change > the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I > am thinking if I need to change tau_t also, since diffusivity constant is > also rel

Re: [gmx-users] md step- structure fragmentation

On 29/02/2012 3:10 PM, priya thiyagarajan wrote: hello sir, I performed simulation for 30ns, because of queue time limit my run terminated at 11.6ns.. i thought of analysing my trajectory file.. so generated pdb file from trr using dump option.. when i visualize the pdb,i noted that my prote

Re: [gmx-users] using more processors for g_mindist

On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjcon

Re: [gmx-users] using more processors for g_mindist

a screwdriver". Mark Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on

Re: [gmx-users] using more processors for g_mindist

r not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 29/02/2012 6:01 PM, aisw

Re: [gmx-users] error

On 29/02/2012 7:28 PM, RAMYA NAGA wrote: Dear friends, iam doing protein-ligand dynamics and i have completed everything.iam running for 2ns. After submitting to cluster,i am getting the error as File input/output error: Cannot rename checkpoint file; maybe you are out of quota? For more inf

Re: [gmx-users] Re: gmx-users Digest, Vol 94, Issue 185

Thank you! > > Bo > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu <http://vt.edu> |

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

On 29/02/2012 9:26 PM, Steven Neumann wrote: On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] quick question about restart

On 29/02/2012 9:47 PM, Anna Marabotti wrote: Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation

Re: [gmx-users] using g_angle

On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. However it produces a .xvg file whe

Re: [gmx-users] using more processors for g_mindist

against all the water within the cut off individually? If you have read g_dist -h and want to ask this question, then I did not understand your previous statement of your objective. Mark Thanks On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote:

Re: [gmx-users] md in vacuo

On 29/02/2012 8:33 PM, Thomas Evangelidis wrote: Dear GROMACS community, I use the following parameters to run MD of ethane in vacuo. Then I calculate the H-C-C-H dihedral angle distribution and from that the rotational energy barrier using the formula DeltG=-k*T*ln(x), where x is the dihedra

Re: [gmx-users] using g_angle

On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abraham: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10

Re: [gmx-users] mdrun -pd

On 1/03/2012 12:31 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to use option -p of mdrun for particle decomposition. I used: mpiexec mdrun -pd -deffnm nvt I obtain: apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead

Re: [gmx-users] using g_angle

ot; -1090.00 -1081.00 -1070.00 Which does what I'm looking for but this means that I'll need a file for each angle. Is there a faster way to get a file that has like two columns, one for the dihedral and another one for the angles? Thanks Francesc

Re: [gmx-users] on the dissociation of protein complex during MD

On 1/03/2012 11:57 AM, Dialing Pretty wrote: Dear All, Some of the complexes of PDB files in RCSB are not from protein-protein interaction, but from the packing of protein crystal. Thus in solution the "protien complex" may dissociate. However as for the protein are usually very large, and I re

Re: [gmx-users] crashed run...

On 1/03/2012 5:30 PM, rama david wrote: Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s -f -e -o -g -cpi -append -v Now is my system is started from the initial time or from the time

Re: [gmx-users] dihedral distributions

On 1/03/2012 5:07 PM, Juliette N. wrote: Hi all, Can anyone guide me how one can obtain dihedral distributions of a polymer chain and how this can be used to ensure the equilibration of system? g_angle takes a list of dihedrals and provides the dihedral distribution of a given dihedral in the

Re: [gmx-users] Random option - genion

On 2/03/2012 4:42 AM, Justin A. Lemkul wrote: Maurício Menegatti Rigo wrote: Dear users, can anyone tell me if the random option (genion program) was set to always stay in the "yes" state? I'm trying to set "-random no" (just a test), but it didn't work at all. The default is "yes." To i

Re: [gmx-users] Segmentation fault - Implicit solvent

On 2/03/2012 9:22 AM, Steven Neumann wrote: On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] mdrun -multi flag

On 2/03/2012 10:15 AM, bo.shuang wrote: Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more

Re: [gmx-users] MDrun append...

On 2/03/2012 3:59 PM, rama david wrote: Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called

Re: [gmx-users] dssp and gromacs version

On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

Re: [gmx-users] [ bondedtypes ]

On 3/03/2012 5:17 AM, Lara Bunte wrote: Hi The first part in a .rtp file is the [ bondedtypes ] with syntax [ bondedtypes ] ; bondsanglesdihedralsimpropers 1 1 1 2 1.) What do this numbers mean? I found nothing in the manual to that

Re: [gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul)

On 3/03/2012 7:34 AM, bo.shuang wrote: Thank you for help! Is that possible to run REMD on a PC with only one processor? No. See http://www.gromacs.org/Documentation/How-tos/REMD Mark Bo bo.shuang wrote: > Hi, Mark, > > Thank you for help. It works. But now I have new fatal error: > > Fata

Re: [gmx-users] do_dssp segmentation fault

On 3/03/2012 5:14 PM, arun kumar wrote: Dear all, Iam trying to generate secondary structure plot through do_dssp program, but there was an error like "segmentation fault" Reading file md.tpr, VERSION 4.0.7 (single precision) Reading file md.tpr, VERSION 4.0.7 (single precision) Segmentation

Re: [gmx-users] Anomalous temperature

On 3/03/2012 5:08 PM, zhongjin wrote: Dear gmx users, It seems that I have found a strange temperature value after NVT equilibrium for 200 ps. I simulate a CNT with two graphite sheets in water box. I do not want to them to deform or change their shaps, So I use a very large position restra

Re: [gmx-users] do_dssp segmentation fault

On 3/03/2012 6:21 PM, arun kumar wrote: yes other gromacs tools are working properly ...i installed gromacs in /usr/local/ so i used the command /usr/local/gromacs/bin/./do_dssp -s md.tpr -f md.xtc -o ss.xpm and i also set the environment variable as export DSSP=/usr/local/gromacs/bin/do_dssp

Re: [gmx-users] problem in using OPLS forcefield parameter in lipid simulation

On 4/03/2012 10:15 PM, Anushree Tripathi wrote: I am not getting the "ffoplsaanb.itp" file for lipid simulation.PLease tell me how to locate the file. It depends on your system and GROMACS version. See http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_i

Re: [gmx-users] cannot determine precision of trn file

On 5/03/2012 8:48 PM, Nidhi Katyal wrote: Dear All, I was running my simulation for 30ns but at the last step i got following error: "Cannot close energy file;it might be corrupt, or maybe you are out of quota." It was found that there was some disk space problem but when the issue was resolv

Re: [gmx-users] Distance between selected atoms during simulation

On 5/03/2012 8:48 PM, James Starlight wrote: Dear Gromacs Users! I want to perform measurements of the distances between backbone as well as side-chain atoms of the selected residues using gro and trajectory files. What Gromacs program should I use for such measurements? Check out manual

Re: [gmx-users] How to answer in this mailing list?

On 5/03/2012 11:39 PM, Lara Bunte wrote: Hello I wrote an email to the mailing list with the subject [ bondedtypes ] and I got answers that helped me. I wanted to answer to this by a new email with same subject and the mailing list create a new question out of it. How do I answer in this mail

Re: [gmx-users] g_msd segmentation fault

On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segme

Re: [gmx-users] segmentation fault err

On 6/03/2012 2:58 AM, shilpa yadahalli wrote: Dear gmx-users, I'm facing "segmentation fault error" while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values,

Re: [gmx-users] folding of coordinates in trajectory files

On 6/03/2012 2:59 AM, Gavin Melaugh wrote: Hi All I was wondering. I assume gromacs writes folded coordinates in the trajectory files. If so does it use rx(i) = rx(i) -boxl *nint(rx(i) / boxl) to fold the coordinates at each step? and where does it define the origin (0,0,0) GROMACS suits it

Re: [gmx-users] cannot determine precision of trn file

On 6/03/2012 12:30 AM, Nidhi Katyal wrote: I think my restart was achieved successfully as my err file contained following lines: "reading checkpoint file state.cpt generated: Loaded with memory making 2D domain decomposition 4*2*1 starting mdrun 'protein in water' 1500 steps, 3.0ps(cont

Re: [gmx-users] g_bar bug with temperature

On 6/03/2012 6:58 PM, Tom Kirchner wrote: Dear all, I made a free energy calculation and want to evaluate my data with g_bar. But when I am using g_bar on my .xvg files I get an error of the form: Temperature in file md_0.35.xvg different from earlier files or setting All simulations we

Re: [gmx-users] Coupling groups

On 6/03/2012 8:21 PM, Steven Neumann wrote: Dear Gmx Users, I am running my protein with ligand. at the begining of my simulation the protein is far away from the ligand. Then in about 5-10 ns my ligand binds to the protein surface remaining there for rest 90-95 ns. Would you adjust coupling g

Re: [gmx-users] Coupling groups

On 6/03/2012 10:40 PM, Steven Neumann wrote: On Tue, Mar 6, 2012 at 11:35 AM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote: On 6/03/2012 8:21 PM, Steven Neumann wrote: Dear Gmx Users, I am running my protein with ligand. at the begining of my s

Re: [gmx-users] how to add custom potential function

On 7/03/2012 2:07 PM, smith bill wrote: i have three custom potential functions to add into gromacs,what's the easiest way to do this? Don't. :-) Use custom lookup tables. See various manual sections. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re: [gmx-users] LINCS problem with EM and Virtual sites

On 8/03/2012 5:05 AM, francesco oteri wrote: Hi gromacs users, I am tying to minimize a protein through grolacs 4.5.5 double precision. If I try to minimize it without virtual site, everythin goes fine but if I add virtual site through: pdb2gmx -vsite hydrogens -chainsep id -f Aqui_model.pdb

Re: [gmx-users] grompp - Group protein not found

On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this

Re: [gmx-users] HOW TO USE SILVER ATOMS IN AMBER99 FORCE FIELD

On 8/03/2012 12:19 AM, Kavosh Zandsalimi wrote: Dear GMX users; I hope you are well. I want to simulate the interactions between DNA and Ag clusters. The problem is that Amber99 ff does not know silver atoms and residues. I have defined Ag and Au in atomtypes.atp and assigned Ag LJ parameters i

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