Re: [gmx-users] g_hbond : normalization autocorrelation function.

gt; > Erik Marklund, PhD > Postdoctoral Research Fellow > Fulford JRF, Somerville College > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ > >> On 19 Jul 2015, at 04:07, Nilesh

[gmx-users] g_hbond : normalization autocorrelation function.

Hello, I am calculating autocorrelation function without normalization using g_hbond g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac ./test/hbac_3.xvg -num ./test/num_3.xvg The output, hbac_3.xvg, don't have normalized auto correlation function. Here is initial part @title

Re: [gmx-users] g_hbond

Hello Erik, I did the same. Thanks, Nilesh > Hi Nilesh, > > You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the > contacts in the last column of hb.xvg. > > Kind regards, > Erik > >> On 10 Jul 2015, at 15:58, Nilesh Dhumal wrote: >>

Re: [gmx-users] g_hbond

I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm? Nilesh > But without contact you will need a full donor-hydrogen-acceptor triad for > it to be registered, which is not what you want as far as I can tell. > > Erik > >> On 10 Jul 2015, at 1

Re: [gmx-users] g_hbond

gt; How many donors and acceptors are found? > > Kind regards, > Erik > >> On 10 Jul 2015, at 14:37, Nilesh Dhumal wrote: >> >> I calculated number of hydrogen bond with cutoff 0.25 nm (Distance >> between >> hydrogen and O,acceptor) using g_hbond, >

Re: [gmx-users] g_hbond

lesh >> >> On 7/9/15 9:13 PM, Nilesh Dhumal wrote: >>>> >>>> >>>> On 7/9/15 9:02 PM, Nilesh Dhumal wrote: >>>>> Hello, >>>>> >>>>> I am calculating g_hbond for water system. I have a question about

Re: [gmx-users] g_hbond

Thanks. I will use two groups. Nilesh > > On 7/9/15 9:13 PM, Nilesh Dhumal wrote: >>> >>> >>> On 7/9/15 9:02 PM, Nilesh Dhumal wrote: >>>> Hello, >>>> >>>> I am calculating g_hbond for water system. I have a question about &g

Re: [gmx-users] g_hbond

> > > On 7/9/15 9:02 PM, Nilesh Dhumal wrote: >> Hello, >> >> I am calculating g_hbond for water system. I have a question about >> specifying two group for calculating hydrogen bond. >> >> Do I specify atoms in triplet(O-H---O)? >> Can I speci

[gmx-users] g_hbond

Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? Default -r cutoff is 0.35nm. Is the distance bet

[gmx-users] HBlife time

Dear Gromacs Users, I am calculating hydrogen bond life time for water system. I have 128 water molecules in the system. The program scan the HB criteria for each OH bond with the rest 127 oxygen (128*128). For single OH bond I have calculated the HB lifetime. If there are more than 1 HB how doe

Re: [gmx-users] append simulation

> > > On 5/4/15 6:08 PM, Nilesh Dhumal wrote: >> Hello Gromacs Users, >> >> I have finished 30ns simulation and I want to run 30ns more. >> If I use append yes, will it append to existing trajectory file. >> Will I get the final 60 ns trajectory. >&

[gmx-users] append simulation

Hello Gromacs Users, I have finished 30ns simulation and I want to run 30ns more. If I use append yes, will it append to existing trajectory file. Will I get the final 60 ns trajectory. Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_

[gmx-users] qm-mm calculation : Gromacs + cpmd

Hello, I am planning to qm mm simulation with Gromacs + cpmd. Can I interface recent gromacs version (4.5.5) with cpmd (3.17.1)? Where can I find the information about interface? Thanks, Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mail

Re: [gmx-users] Fatal error:No molecules were defined in the system

oval. The reason it is being held: Message body is too big: 58940 bytes with a limit of 50 KB > > On 10/20/14 11:19 AM, Nilesh Dhumal wrote: >> Hello, >> >> For grompp >> >> grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr >> >> I get the

[gmx-users] Fatal error:No molecules were defined in the system

Hello, For grompp grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr I get the error" Fatal error:No molecules were defined in the system" Here I pasted initial part of test.top file. ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs

Re: [gmx-users] pdb2gmx ffG43a1 force field

CACB CC HM gd_101 CCCB CC HM gd_101 OACA CB CC gd_102 OBCA CB CC gd_102 > > On 10/17/14 4:09 PM, Nilesh Dhumal wrote: >> Hello, >> >> I am generating .top file using pdb2gmx and choose ffG43a1 force field >> from the list. &

[gmx-users] pdb2gmx ffG43a1 force field

Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96

[gmx-users] pdb2gmx ffG43a1 force field

Hello, I am generating .top file using pdb2gmx and choose ffG43a1 force field from the list. pdb2gmx is running for an hour. Here I pasted the last part appeared on screen Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96

[gmx-users] .gro file units

Hello, I am converting .trr file to .gro file. trjconv -f structure_1.trr -s structure_1.tpr -pbc nojump -o structure_1.gro What are the unit of coordinate in .gro file? Is it angstrom? Thanks, Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] grompp Segmentation fault

0. 0. 1BTC CC3030 22.768 16.737 21.072 0. 0. 0. > > On 10/13/14 10:42 PM, Nilesh Dhumal wrote: >> hello, >> >> I running grompp for simulation. I get Segmentation fault error. >> >> grompp -f 600.mdp -c cu.gro -p cu_btc_1.

[gmx-users] grompp Segmentation fault

hello, I running grompp for simulation. I get Segmentation fault error. grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr checking input for internal consistency... processing topology... Segmentation fault Could any one tell what is the problem? Thanks, Nilesh -- Gromacs Users mailin

[gmx-users] Fatal error: Atom O in residue BTC 1 not found in rtp entry with 156 atoms while sorting atoms

Hello, I am getting a following error for pdb2gmx. Fatal error: Atom O in residue BTC 1 not found in rtp entry with 156 atoms while sorting atoms Could anyone tell whats going wrong? Nilesh Here is initial part of .pdb file TITLE Title REMARKTHIS IS A SIMULATION BOX CRYST1

[gmx-users] Velocities from checkpoint

Hello, I am running 30ns simulation divided into 30 1ns simulations. I am saving the velocities each 5fs and I can't run a single 30ns simulation with saving velocities each 5 fs. I am running 30 simulations,each is 1ns. I get the velocities and delete the trajectory and go for next simulation.

[gmx-users] Reactive force field

Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- 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_L

[gmx-users] Reactive force field

Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- 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

[gmx-users] translational dipole moment during the simulation

Hello, I am calculating rotational and translational part of dipole moment. For translational dipole moment I want to save the velocities each 5fs and for rotational part I want to update trajectory each 2ps. I am running 30ns simulation. The size of trajectory is big and simulation get crashed be

Re: [gmx-users] berendsen vs parrinello-rahman

same error. After changing pressure coupling from parrinello-rahman to berendsen , both the simulations went well. Nilesh > Unstable models or unstable initial conditions will behave unpredictably. > Unfortunately you've not given us much to go on. > > Mark > On May 16, 2014 6:0

Re: [gmx-users] berendsen vs parrinello-rahman

> > > On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: >> Hello, >> >> I am running the simulation for ionic liquids. I initially did >> simulation >> with Gromacs VERSION 4.0.7 with "parrinello-rahman" pressure coupling. >> Here I pa

[gmx-users] berendsen vs parrinello-rahman

Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with "parrinello-rahman" pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system r

Re: [gmx-users] g_dipoles

> On 2014-05-11 02:18, Nilesh Dhumal wrote: >> I run g_dipoles for two ionic liquids : 1-Ethyl-3-methylimidazolium >> chloride and 1-Ethyl-3-methylimidazolium ethylsulfate. In both the >> systems >> cation is common 1-Ethyl-3-methylimidazolium. > > > I didn

Re: [gmx-users] g_dipoles

f mass */ for(a=a0; a > On 4/27/14, 4:33 PM, Nilesh Dhumal wrote: >>> >>> >>> On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: >>>>> >>>>> On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: >>>>>> Hello, >>>>>>

Re: [gmx-users] g_dipoles

> > > On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: >>> >>> On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: >>>> Hello, >>>> >>>> I run g_dipoles for two different systems (System are ionic liquids). >>>> >>>> For one s

Re: [gmx-users] g_dipoles

> > On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: >> Hello, >> >> I run g_dipoles for two different systems (System are ionic liquids). >> >> For one system when I run g_dipoles I get following message >> >> There are 256 molecules in the selection >

[gmx-users] g_dipoles

Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get

[gmx-users] Dipole moment calculations

Hello, How does Gromacs calculate the dipole moment? Does it calculate the distance of a atom from origin (0.0,0.0,0.0) or distance from center of box (box_length/2, box_length/2, box_length/2) Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] g_current

6 51.7085 49.994-2.23022 51.6964 49.995-2.25746 51.6842 49.996-2.27946 51.6718 49.997-2.29797 51.6592 49.998 -2.3135 51.6466 49.999-2.32483 51.6339 50.000-inf 51.6211 Nilesh > > On 4/15/14, 2:2

Re: [gmx-users] g_current

0.584 3.07 100 HW1 SOL 34 0.04 -0.0643 1.88 0.849 196 HW1 SOL 66 0.04 1.8 1.92 -0.0014 219 OW SOL 74 0.105 3.03 1.97 0.61 221 HW2 SOL 74 0.043.08 2.05 0.649 238 HW1 SOL 80 0.041.33 2.99 -0.0012 (maybe more) > > > On 4/15/14, 2:18 P

Re: [gmx-users] g_current

I checked with gmx_check, its says velocities found. Nilesh > > > On 4/15/14, 11:50 AM, Nilesh Dhumal wrote: >> Hello, >> >> >> I am trying to calculate the correlation of the rotational and >> translational dipole moment of the system using g_current.

[gmx-users] g_current

Hello, I am trying to calculate the correlation of the rotational and translational dipole moment of the system using g_current. There are 864 water molecules in the system. I run the following command, but its not writing the mc.xvg. g_current -f water.trr -s water.tpr -mc Could you tell wha