[gmx-users] water in bulk

Dear All, Does Gromacs have a tool to calculate how many water molecules dissolve into the bulk of an organic solvent (let's say, 5 Angstrom from protein surface in the box)? Many thanks in advance. Regards, Jennifer -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] water in bulk

that satisfy, then that's your answer. Mark On Wed, Jun 17, 2015 at 2:44 PM Jennifer Vo quyvio...@gmail.com wrote: Dear All, Does Gromacs have a tool to calculate how many water molecules dissolve into the bulk of an organic solvent (let's say, 5 Angstrom from protein surface in the box

[gmx-users] g_hbond on trajectory

Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg The log file showed me:

Re: [gmx-users] g_hbond on trajectory

Thank you, Justin. Jennifer On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/2/15 5:01 AM, Jennifer Vo wrote: Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md

Re: [gmx-users] Number Error in XTC file

). Mark On Tue, Apr 28, 2015 at 4:20 PM Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got the error in the end of trajectory converting: Magic Number Error in XTC file (read -335790888, should be 1995) trjconv -s md-1.tpr -f md-300ns-wat.xtc -o md_CA.pdb -n index_8pro.ndx -pbc

[gmx-users] Number Error in XTC file

Dear All, I have got the error in the end of trajectory converting: Magic Number Error in XTC file (read -335790888, should be 1995) trjconv -s md-1.tpr -f md-300ns-wat.xtc -o md_CA.pdb -n index_8pro.ndx -pbc mol -ur compact -center -skip 1000 Is there anybody know what`s the error about? Many

Re: [gmx-users] Water TIP4Pnew and topology file

for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jennifer Vo quyvio...@gmail.com Sent: Wednesday, April 08, 2015 10:46 AM To: gmx-us...@gromacs.org Subject: [gmx

[gmx-users] diisopropylethylene topology

Dear All, Does anyone has the itp file for diisopropylethylene? It would be very helpful if you can share. Many thanks in advance. Regards, Quy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] g_rotacf and P 1,2,3 meaning

Dear All, When using g_rotacf, could you please explain to me the difference between option P 1, 2, and 3? The results from these are significantly different. Many thanks in advance. Regards, Jennifer -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to interpret g_principal output calculates

Dear All, I am trying to analyze how protein rotating in a mixture of organic solvent and water. I thought g_principal could help by checking the (xyz) of the whole protein over the time. The output gave 4 x.xvg files and I am not sure how to interpret them. Can I see the movement of protein by

Re: [gmx-users] why rotational correlation function decays to negative

of time. This may indicate that there are harmonic motions involved. Hope it helps, Tsjerk On Wed, Mar 4, 2015 at 11:01 AM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I calculated rotational correlation function by g_rotacf and saw the autocorrelation function started at 1 for t

Re: [gmx-users] solvate with an exact number of solvent molecules

Hi Rebeca, In GROMACS 5.0, I use gmx insert-molecules -f your.gro -ci your_insert.gro -o output.gro -nmol xxx where xxx is the number you want. Hope it helps. Jennifer On Mon, Mar 2, 2015 at 6:44 PM, Rebeca García Fandiño rega...@hotmail.com wrote: Dear GROMACS users, I am trying to do a

Re: [gmx-users] multiple ligands topology

/16/15 3:49 AM, Jennifer Vo wrote: Dear Justin, Many thanks again. I just define a small box then insert molecules and let it floating nearby the protein, then redefine the actual box for the real concentration of protein. The maxwarn 27 is from this NOTE 1 [file em_ion.mdp]: With Verlet

[gmx-users] multiple ligands topology

Dear All, I am running a simulation for a systems including two chains of proteins and two ligands using amber 99SB ff. My topol.top is #include amber99sb.ff/forcefield.itp #include my_ligand_atomtypes.itp ; Include chain topologies #include A.itp #ifdef POSRES #include posre_A.itp #endif

Re: [gmx-users] multiple ligands topology

...@vt.edu wrote: On 2/13/15 6:03 AM, Jennifer Vo wrote: Dear All, I am running a simulation for a systems including two chains of proteins and two ligands using amber 99SB ff. My topol.top is #include amber99sb.ff/forcefield.itp #include my_ligand_atomtypes.itp ; Include chain topologies

Re: [gmx-users] multiple ligands topology

, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 9:59 AM, Jennifer Vo wrote: Dear Justin, Many thanks for your kind answer. The output of minimization for Protein + 1 Ligand Steepest Descents converged to Fmax 100 in 868 steps Potential Energy = -8.0409740e+06 Maximum force

Re: [gmx-users] topology and parameter set up

: On 2/2/15 6:37 AM, Jennifer Vo wrote: Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name

[gmx-users] topology and parameter set up

Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma

Re: [gmx-users] Atomtype P,SI not found from grompp

; P, SI - OA - CHn, P 95 in file gromos54a7.ff/ffbonded.itp. It means it's not a new atom type, did I interpret correctly? Regards, Jennifer On Fri, Jan 23, 2015 at 5:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/23/15 9:52 AM, Jennifer Vo wrote: Dear Justin, I did try

Re: [gmx-users] Atomtype P,SI not found from grompp

Dear Justin, Now I get it. Thanks a lot for taking your time. I sent the email to the author of ATB developer and still waiting for the answer. Many thanks again. Regards, Jennifer On Fri, Jan 23, 2015 at 5:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/23/15 11:51 AM, Jennifer Vo wrote

Re: [gmx-users] Atomtype P,SI not found from grompp

in advance. Regards, Jennifer On Thu, Jan 15, 2015 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 1:58 PM, Jennifer Vo wrote: Dear Justin, Thanks again! I have downloaded the topology from Automated Topology Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using

[gmx-users] Atoms in the .top are not numbered consecutively from 1

Dear All, I have got this error after running grompp Fatal error: Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 4, while at-nr = 2) My topology file is ; Include forcefield parameters #include gromos54a7.ff/forcefield.itp ; Include ligand topology #include

Re: [gmx-users] Atoms in the .top are not numbered consecutively from 1

. Regards, Jennifer On Fri, Jan 23, 2015 at 5:13 PM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got this error after running grompp Fatal error: Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 4, while at-nr = 2) My topology file is ; Include forcefield

[gmx-users] Too many LINCS warnings

Dear Experts, I am running an nvt equilibration for a System including 2 Proteins and 2 ligands. I have got this error: *Fatal error:Too many LINCS warnings (1000)If you know what you are doing you can adjust the lincs warning threshold in your mdp fileor set the environment variable

Re: [gmx-users] Atomtype P,SI not found from grompp

Dear Justin, Many thanks. It's clear to me now. I will contact them for this issue. Regards, Jennifer On Thu, Jan 15, 2015 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 1:58 PM, Jennifer Vo wrote: Dear Justin, Thanks again! I have downloaded the topology from Automated

Re: [gmx-users] Atomtype P,SI not found from grompp

nap_allatom.itp: 26 P,SI1NAP PN52.259 30.9738 should I change P,SI to P only? Regards, Jennifer On Thu, Jan 15, 2015 at 7:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 12:57 PM, Jennifer Vo wrote: Dear Justin, Many thanks for your answer. I tried grep SI

Re: [gmx-users] Atomtype P,SI not found from grompp

all of these have the P,SI type. I would like to ask for your advice in this case. Regards, Jennifer On Thu, Jan 15, 2015 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 1:31 PM, Jennifer Vo wrote: Dear Justin, Thanks a lot, now I got it. I thought P and SI is the two separated

[gmx-users] Atomtype P,SI not found from grompp

Dear Experts, I ran a grompp (gromos53a6 ff) grompp -f em.mdp -c complex2_solvated.gro -p topol.top -o complex.tpr and it generated the error Atomtype P,SI not found I checked the gromos53a6.ff/atomtypes.atp and see there are P, SI in the list SI 28.08; Silicon P 30.97380 ;

Re: [gmx-users] Atomtype P,SI not found from grompp

Dear Justin, Many thanks for your answer. I tried grep SI *.* in the whole working directory but nothing found. Where could it be if I have to search? Thanks a lot again. Regards, Jennifer On Thu, Jan 15, 2015 at 6:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 12:20 PM, Jennifer Vo

[gmx-users] trjconv mismatch

Dear All, I have got this error while running trjconv from .xtc to .pdb file. The System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is the total number of Atoms in the System. The index.ndx was created from md.gro file, and I Chose #1 for Protein. I don't know where is the

Re: [gmx-users] trjconv mismatch

index.ndx and chose #1 for Protein. Many thanks for any help! Regards, Jennifer On Wed, Jan 14, 2015 at 9:09 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got this error while running trjconv from .xtc

[gmx-users] trjconv mismatch in number of atoms

Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I don't know where the origin of the

[gmx-users] gmxcheck killed

Dear All, My command was: *gmxcheck_mpi -f md-1.trr -n index.ndx -s1 em-1.tpr -c md-1.gro -e md-1.edr -m md1-gmxcheck.txt* The output md1-gmxcheck.txt content was: *\section{Methods}\subsection{Simulation system}A system of 70256 molecules (1087816 atoms) was simulated.*