Re: [gmx-users] ions.itp file for polarized ions

Thank you very much David Cuong On 18 February 2013 17:40, David van der Spoel wrote: > On 2013-02-18 10:16, Cuong Nguyen wrote: > >> Dear Gmx-users, >> >> I have ions.itp file for polarized Na+ and Cl- as follows: >> >> >> ; Sodium, Na+ >&g

[gmx-users] ions.itp file for polarized ions

Dear Gmx-users, I have ions.itp file for polarized Na+ and Cl- as follows: ; Sodium, Na+ [ moleculetype ] ; molnamenrexcl Na+1 [ atoms ] ; idat typeres nrresidu nameat namecg nrcharge 1Nac1Na+Nac11+0.312403 2Nas1Na+

Re: [gmx-users] force field

, Justin Lemkul wrote: > > > On 12/5/12 8:29 PM, cuong nguyen wrote: > >> Thanks for your email Justin. >> >> I remember you answered an email that there is a PRODRG server working >> with >> higher version of Gromos87. Could you show me the link please?

Re: [gmx-users] force field

, CTAB and triton x45. Best regards, Van On 5 December 2012 20:00, Justin Lemkul wrote: > > > On 12/4/12 10:22 PM, cuong nguyen wrote: > >> Dear gmx users, >> >> i have got the coordinate and topol files of nonanol from the server: >> http://davapc1.bioch.du

Re: [gmx-users] Temperature Histogram

Dear, Thanks a lot for your suggestion Justin. I have a box 3 3 20 and want to plot the temperature along the z axis. I did the commands: g_energy -f NVT_20ns.edr -s topol.top -o temp g_analyze -f temp.xvg -dist temp.xvg and got the results: 281.9 0 282 0.000149997 282.1 0 282.2 0 282.3 0

Re: [gmx-users] Lennard-Jones Parameters

Dear, The top file downloaded from PRODRG did not consist of [atomtypes]. Please tell me how can I add and use this function? Best regards, Cuong On 15 October 2012 16:43, Peter C. Lai wrote: > Is there no [atomtypes] section in the top file? > > On 2012-10-15 03:53:54PM +0800, cuo

Re: [gmx-users] Lennard-Jones Parameters

meters, so if you need > to change the LJ parameters, edit the top file it gave you. > > If you want to reproduce the results of a published paper, you should use > the > forcefield and parameters specified in that paper and contact the author(s) > if more details are needed. >

Re: [gmx-users] Lennard-Jones Parameters

Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule? Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul wrote: > > > On 10/12/12 8:04 AM, cuo

[gmx-users] mdrun-gpu

Dear Gromacs Users, I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support. when I run grompp-gpu to generate the .tpr file, it worked well: grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96 however, then I run mdrun-gpu "mdrun-gpu -s min -o min -c min.g96 -x min -e min -g min", it was stopped

[gmx-users] genconf command

Dear Gmx-users, I created a box size 4 4 2 and named layer.gro. Then "genconf" was used to doulble this box: genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8 However, the copied box has the same direction as the original box. Could you please help me to rotate 180 degrees the copied one

[gmx-users] Calculate surface tension

Dear Gromacs Users, I am trying to calculate the surface tension at air/water interface of water model SPC/E. I used the command g_energy and chose #surfacetension. However, the output file was like this: 0 14001.49219 0.5 21139.67773 1 7328.798828 1.5 16114.55664 2 8224.392578 2.5 16558.3

Re: [gmx-users] Index selection in g_potential

Hi, if you want to calculate the potential of some groups (0, 3, 11), using make_ndx to creat a new group consisting of these groups. Then running g_potential. Cuong 2012/5/16 Andrew DeYoung > Hi, > > I am using the utility g_potential. It takes (among other files) an index > file. At the

[gmx-users] Getting local pressure

Dear, Could anyone please let me know, in Gromacs analysis is there any way to get the local pressure (along z-axis of the box)? Thanks a lot! Cuong Nguyen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Box of water

n 4/30/12 10:02 PM, cuong nguyen wrote: > >> Dear Gromacs Users, >> >> I used the command "genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 >> 3 10" >> to create box of 3010 water molecules. However, now I need to create a >> same size >&

[gmx-users] Box of water

Dear Gromacs Users, I used the command "genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10" to create box of 3010 water molecules. However, now I need to create a same size box with only 846 water molecules. Please help me to do this. Thanks, Cuong -- gmx-users mailing listgmx-users

[gmx-users] mpirun

Dear Gromacs Users, as in the manual, I tried to run the simulation on 4 processors and used the command as follow: *mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x NVT_50ns -e NVT_50ns -g NVT_50ns -v* Then I got the error: *mpirun was unable to launch the specified application

Re: [gmx-users] using MPI

wever, you will need mpi. > > Best, > > Erik > > 15 mar 2012 kl. 04.50 skrev cuong nguyen: > > Dear Gromacs users, > > I prepare to run my simulations on the supercomputer on single node with > 64 CPUs. Although I have seen on Gromacs Mannual suggesting to use MPI

Re: [gmx-users] genbox

You can use the command genbox -cs with the option -maxsol number to specify the number of water molecules Good luck Cuong 2012/1/16 vidhya sankar > Hello Justin, > Thanks for your patient reply > > I would like to solvate my molecules with specific > number

Re: [gmx-users]-Snapshots

Thanks a lot Justin. I have just used trjconv -dump with the command "trjconv -s NVT_final2ns.tpr -f NVT_final2ns -o trjconv.gro -dump 1" to extract a frame. However, I still do not know how to get the snapshot like a 3D picture . Please help me! Many thanks Cuong Nguyen 2012/1/1

[gmx-users]-Snapshots

Dear Users, Please let me know if we can get snapshot from GROMACS. I am using version 4.4. Thanks and best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

[gmx-users] CTAB force field

Dear all, I prepare to do simulation about the solution of CTAB. Does anyone know the force field (top and gro files) of CTAB which were published before? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- gmx-users ma

Re: [gmx-users] No such moleculetype Na

Hi Setare, You should find the ions.itp file in your computer, open and see the exact name of sodium in this file. Use this name when using the command "genion". Good luck! Cuong 2011/12/10 Setare Jiji > Hi, > > I am running Tutorial 1: Lysozyme in > Water

[gmx-users] itp file for D2O

Dear GROMACS users, I usually use spce.itp file for water solvent in my simulation. However, now I want to change this solvent to deuterium monoxide (D2O). Please let me know if I have to change this itp file? if yes, where can I find this file? Thank you very much. Best regards, Nguyen Van C

[gmx-users] how to know the pH of a solution

Dear, I have made a 10x10x10 box with 200 hexanoic acid molecules and fill full of water. Please let me know how can I do to know and change the pH of this solution? Thank you very much. Cheers, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- gmx-us

[gmx-users] Adding ions using "genion"

Dear, I create a box of water with 10 MIBC molecules on two opposite surfaces. then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to creat .tpr file before using the command "genion -s min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ and 20 Cl- into this bo

[gmx-users] Create gro and top file for hexanoic acid

Dear Sir/Madam, I have tried to creat the gro and top file for acid hexanoic by using the PRODRG server. However, the atom H in -COOH group could not be found and two O atoms are the same. [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge

Re: [gmx-users] how to make topol.top file for mixed solution

on.* *For more information and tips for troubleshooting, please check the GROMACS * *website at http://www.gromacs.org/Documentation/Errors * Please help me to correct these errors. Thank you very much best regards, Cuong 2011/11/7 Justin A. Lemkul > > > cuong nguyen wrote: > >> D

Re: [gmx-users] how to make topol.top file for mixed solution

file to this system. Thanks a lot. Best regards, Cuong 2011/11/7 Justin A. Lemkul > > > Justin A. Lemkul wrote: > >> >> >> cuong nguyen wrote: >> >>> Dear, >>> >>> I would like to create a solution of mix substances (hexanol an

[gmx-users] how to make topol.top file for mixed solution

regards, Cuong Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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 before

Re: [gmx-users] Regarding Table Extension

Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please help me. Thank you very much. Best rega

[gmx-users] how to make top and gro file for acid hexanoic

Dear, I have used JME in PRODRG to draw acid hexanoic molocule. However, after running, the H atom in -OH could not be created and two oxygen atom were the same. Please tell me what are the errors? Many thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re: [gmx-users] Gromacs inquiries

1, it will run well but I do not know if this box is full. Please help me to change this instruction. Thanks a lot. Regards, Cuong 2011/10/26 Mark Abraham > On 26/10/2011 1:46 PM, cuong nguyen wrote: > >> Dear, >> >> Thanks a lot for useful software. I am trying to g

[gmx-users] Gromacs inquiries

Dear, Thanks a lot for useful software. I am trying to generate a box (4 4 4) with full hexanol molecules inside. I have used the instruction "genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top", however it has not been successful. Please correct the instruction for me or give me any ad