[gmx-users] Hydroixde Ion

, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park PA 16802 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search befo

Re: Re: [gmx-users] Hydroixde Ion

in my methanol-water system. The confusion I have is: The .gro file has OH but is gromacs really accounting OH as 2 atoms? Also, the difference (12519-12487) is greater than 8. Kindly help. Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University

Re: Re: Re: [gmx-users] Hydroixde Ion

(5his8_meohi_wat.gro, 12487) does not match topology (topol.top, 12519) The .top file includes tip4p.itp, methanol.itp and ions.itp. So I am totally confused as to where I am going wrong. Please guide. Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park

Re: Re: Re: Re: [gmx-users] Hydroixde Ion

ions I added 8 chloride ions. And everything works perfectly! So, I think its something with the hyrdroxide ion. I will try adding hydroxide ions using genbox. I think then I need to treat it as a charged residue and have it included in the .rtp file, correct? Thanks, Shivangi Shivangi Nangia

[gmx-users] Placing ions at a required distance

Hello, I am a new gromacs user. I want to place Li+ ions at a required distance from the polypeptide ( which is at the centre of a box of water) I searched through the archive and the manual if there is a way/provision to do this, but could not. Is there a way? Please guide. Thanks, Shivangi

Re: [gmx-users] Placing ions at a required distance

3:26 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello, >> >> I am a new gromacs user. >> >> I want to place Li+ ions at a required distance from the polypeptide ( >> which is at the centre of a box of water) >> >> I s

Re: [gmx-users] Placing ions at a required distance

Thanks, I did it manually using 'cat'. Thanks for your time. -Shivangi On Mon, Mar 28, 2011 at 4:47 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi again, >> >> I did not quite understand the suggestion. >> I have successfully ad

[gmx-users] Check for bad contacts and/or reduce the timestep.

Hello gmx-users, I have a 5 ang box with equal number of water and methanol molecules (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall +2 charged. I am trying to to do a NVT equilibration which runs into the following error: t = 0.000 ps: Water molecule startin

Re: [gmx-users] Check for bad contacts and/or reduce the timestep.

Hello, I am sorry, I did mean 5 nm box. I did do the energy minimization but somehow overlooked the error message at that stage. Things seems to be working now. Thanks for the time. Shivangi On Tue, Mar 29, 2011 at 2:06 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: &

[gmx-users] autocorrelation functions

Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to m

[gmx-users] autocorrelation functions

Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to mo

[gmx-users] NPT equilibration

Hello, I am having problems in carrying out a NPT equilibration of my system at 500 K. System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid anion. NVT equilibration gives expected results. When I load the npt.gro file in VMD, its seems as if the molecules have fragmented/vap

[gmx-users] mdrun segmentation fault

Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydr

[gmx-users] mdrun segmentation fault

Hello gmx users, My system for NVT equilbration runs into segmentation fault as soon as I try to run it. It does not give any warning or hint of what might be going wrong. Since I am a new user I am having difficulty exploring the plausible reasons. System: Protein( polyhistidine), 20 2,5-dihydr

[gmx-users] Placing anion/cation at a particular distance from peptide

Dear gmx users, I need to design a starting configuration of a polypeptide with charged side chains sitting in a box of water with Cl- ions within 7 ang of its radius. I realize that in such a system like charges will essentially prefer to be as far as possible from each other, but I still need t

[gmx-users] ordering components of system using trjorder

Dear gmx-users, I wish to order the components of my system with respect to the polypeptide using trjorder. I want to select my first group as the protein and the second group to be ordered is non-protein (i.e all other components in the system except polypeptide) the command I am using is: tr

[gmx-users] trjorder not working

Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water

[gmx-users] how to get higher precision values for g_velacc

Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

Re: [gmx-users] trjorder not working

accordance with the COM of the polypeptide, I chose -da 0. Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham wrote: > On 4/29/2011 4:08 AM, shivangi nangia wrote: > >> Hello all, >> >> I am trying to order the TIP4P water molecules in my syste

[gmx-users] mdrun Fatal error: Domain decomposition does not support simple neighbor searching

Dear gmx-users, I have a cube (8 nm) of the system containing 1:1 :: water: methanol, a polypeptide, Li ions and 2,5-dihydroxybenzoic acid anions. I am heating this system with no PBC ( evaporation). The md.mdp file is: ; Run parameters integrator = md ; leap-frog integrator nsteps =

Re: [gmx-users] trjorder not working

ery confused about using trjorder, it will be really helpful if someone or Mark can help me understand. Thanks a lot SN On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham wrote: > On 4/29/2011 11:29 AM, shivangi nangia wrote: > > Hello, > > The manual explaining trjorder says: > &g

Re: [gmx-users] trjorder not working

the system get ordered with respect to the protein? or I have have to play around ordering them one by one? Thanks, SN On Thu, May 5, 2011 at 4:37 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello, >> >> Came back to the set of calculations I wa

[gmx-users] sphere around a protein

Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions. Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option generated a cyclinder around the p

Re: [gmx-users] sphere around a protein

cut-off. How can I resolve this? help needed. Thanks, SN On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi Justin and other gmx-users, >> >> I want to make a sphere around a protein (5nm).with Li ions and anions. >>

Re: [gmx-users] sphere around a protein

Dear Justin, No. I am still preparing the system. I want the protein in the solvent sphere. On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello, >> >> Thanks Justin, I am getting somewhere but still running into prob

Re: [gmx-users] sphere around a protein

, May 8, 2011 at 9:53 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Dear Justin, >> >> No. >> >> I am still preparing the system. I want the protein in the solvent sphere. >> >> >> > I see now. You're setti

[gmx-users] -ci option

Dear gmx users, I want to insert few ions in my system randomly. -ci option does that, but I want various "different" random configurations of the ions in my system. Using -ci option does randomly place ions but at the same coordinates each time. Is there a way to randomly generate various conf

Re: [gmx-users] sphere around a protein

:21 AM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi Justin, >> >> I used 15 nm cubic box and 6 nm shell. >> I again tried to insert only 1 histidine molecule in the sphere. I get the >> same error >> >> Fatal error: >> One

Re: [gmx-users] sphere around a protein

which 6sys.gro is sitting. How can I place all the anions and then Li+ ions specifically inside the sphere? Thanks a lot, SN On Wed, May 25, 2011 at 1:18 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi Justin, >> >> >> Revisiting some of th

Re: [gmx-users] sphere around a protein

the ions that I had added in the box? Some might still be in open space of the box? Thanks, SN On Wed, May 25, 2011 at 3:43 PM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> shivangi nangia wrote: >> >>> Hi Justin, >>&

[gmx-users] Fatal error: Not enough memory. Failed to realloc

Dear gmx-users, I was carrying out a continuation of an NPT equilibration from NVT. As soon the job started it ran into the following error: Fatal error: Not enough memory. Failed to realloc 1488624 bytes for nl->shift, nl->shift=0x0 (called from file ns.c, line 101) What is the error about?

[gmx-users] Solvating dodecahedron

Hello All, I am trying to solvate a protein sitting in a dodecahedron using genbox. It gets solvated but a box of solvent is created around the protein. I want the protein to be sitting in a dodecahedron filed with solvent. I used the following commands: editconf -f onlyhis.gro -bt dodecahedro

[gmx-users] Reducing density using -vdwd option for a new solvent in the system

Hello dear gmx-users, I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the solvent ( with a positively charged protein and few DHB anions) in a box. I have created the .itp and .gro file of DHB using PRODRG. I am able to create the system, but when I try to energy minimiz

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

Thanks Justin, vdwradii.dat suggestion worked :) On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello dear gmx-users, >> >> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as >> the solvent

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

. Please guide. Thanks, SN On Tue, Jun 14, 2011 at 11:29 AM, shivangi nangia wrote: > Thanks Justin, vdwradii.dat suggestion worked :) > > > > > On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul wrote: > >> >> >> shivangi nangia wrote: >> >>

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

113 15.9994 16 H 1 DHB HAC 40.031 1.0080 If I have the water/methanol or water:methanol in the system as the solvent, the system runs fine. Please help. Thanks, SN On Tue, Jun 14, 2011 at 3:13 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrot

Re: [gmx-users] Regarding g_dist -dist option

On Fri, Jun 24, 2011 at 10:45 AM, bipin singh wrote: > Hello, > I just want to ask that in g_dist module, -dist option expect distance as a > real argument, so the distance should be in nm or A for that... > -nanometer (nm) > > -- > --- > *Regards,* > Bipin Singh > > > -- >

[gmx-users] building a new molecule which does not exist in gmx data base

Dear Justin and other gmx-users, As per the journal article, Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not assign charges compatible with GROMOS force field. PRODRG 2.5, however, assigns the correct atom types and bonded parameters.

[gmx-users] mpirun and no pbc

Dear gmx-users, I am heating my system at 300 K. I have set the pbc conditions as "no" I get the following error: --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5436 Fatal error: pbc type no is not supported with domain

[gmx-users] branched polyhistidine chain

Hi gmx-users, Is there a way to create a branched polyhistidine chain using gromacs, instead of a straight chain? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mail

[gmx-users] genbox -shell

Hi All, I have a question about genbox -shell option. The online manual says: *-shell* real 0 thickness of optional water layer around solute The value specified for -shell option, example 3, produces a sphere with radius 3 nm or diameter 3 nm? Thanks, SN -- gmx-users mailing listgmx-us

[gmx-users] to find out number of solvent molecules within certain radius of the protein

Dear gmx-users, I wish to calculate the number of solvent molecules within certain radius of the protein all through the trajectory. Is there any utility available with gromacs to do so? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] to find out number of solvent molecules within certain radius of the protein

Hi, Where can I find the documentation for g_select? Thanks, SN On Tue, Jul 26, 2011 at 6:07 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Dear gmx-users, >> >> I wish to calculate the number of solvent molecules within certain radius >

[gmx-users] Extracting .gro file from a crashed run

Hello dear users, I was running a simulation which crashed (without writing output.gro file) Is there a way to extract the .gro file somehow from .trr or any other file? Please guide. Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us