[gmx-users] There was 1 error in input file(s)

Hi everybody I want to build a simulation box fill of water and some SDS molecules. To do this at first I fill the box with SDS molecules without their Na+ ions. Then I filled the simulation box with water molecules. After that, I want to replace some water molecules with Na+ ions. I ran the follo

[gmx-users] Segmentation fault

Hi all Would you please let me know how can I remove the following error when I want to run 'mdrun -v -deffnm H'? Back Off! I just backed up H.log to ./#H.log.1# Getting Loaded... Reading file H.tpr, VERSION 4.5.4 (single precision) Starting 24 threads Segmentation fault Thanks Regards Saly -

[gmx-users] genbox,genconf

Hi all Would you please let m eknow f we use 'genconf' after that we must use 'genbox' before applying 'grompp'? Thanks Regards Saly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppo

[gmx-users] genconf, grompp

Hi all When we want to fill a box containing for example 6 molecules we can not use genbox. We have to use genconf to build it. genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro When I use this command as I want a box including 6 molecules are filled When I open .gro file of the fille

[gmx-users] genconf, grompp

Hi all When we want to fill a box containing for example 6 molecules we can not use genbox. We have to use genconf to build it. genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro When I use this command as I want a box including 6 molecules are filled When I open .gro file of the fille

[gmx-users] genconf,grompp

Hi all In the following you can see the format of H-largebox.gro including my desired number of atoms, but when I apply the following grompp command with and with out maxwarn I see the following error: --- Program grompp, VERSION 4.5.4 Source c

[gmx-users] genconf, grompp

Hi everybody After using genconf to build a .gro file for example containing 10 molecules, I want to use grompp to minimize the system as the following: genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1 Although I s

[gmx-users] 'genconf'

Hi Thanks alot. With your suggestions my problem was solved. Saly -- 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 posting! Please don't post (un)subscr

[gmx-users] (no subject)

Hi Thanks alot. With your suggestions my problem was solved. Saly -- 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 posting! Please don't post (un)subscr

[gmx-users] genconf

Hi all I used genconf and genbox command as the following: genconf -nbox 50 50 40 -f H.gro -nmolat 100 -o H-box.gro genbox -cs H-box.gro -nmol 10 -box 100 100 100 -p topol.top -o H-box_new.gro But I received: Reading solvent configuration "Great Red Owns Many ACres of Sand " solvent confi

[gmx-users] genconf

Hi all As Justin said to fill a box with 8 molecules I should construct small boxes containing for example some hundred molecules with 'genconf' and then build a big box including 8 molecules. Now I want to know how can I use 'genconf' and then genbox, instead of the following command (Onl

[gmx-users] not allocate memory and genconf

Hi Justin According to the following you said that I should use genconf. Would you please help me to use it? Would you please tell me instead of the following command: genbox -ci H.gro -nmol 8 -box 300 300 300 -p topol.top -o H-box.gro Which command I should use including genconf and genbo

[gmx-users] 'not allocate memory'

Hi I think the error is not a reason of less memory of my computer. Because in a supercomputer I see the hollowing error too. Genbox could be run if I choose the number of atoms less than 5000. Thanks Saly Try 824box_margin = 0.45 overlap: Neighborsearching with a cut-off of 0.45 Table routine

[gmx-users] 'not allocate memory'

Hi, I want to add 8 of a molecule including 6 atoms. But when I run each of the following commands: genbox -ci H.gro -nmol 8 -box 15 15 15 -p topol.top -o H-box.gro genbox -ci H.gro -nmol 8 -box 100 100 100 -p topol.top -o H-box.gro genbox -ci H.gro -nmol 8 -box 150 150 150 -p to

[gmx-users] (no subject)

Hi, I want to add 8 of a molecule including 6 atoms. But when I run each of the following commands I System total charge: 0.000 Grid: 5 x 5 x 5 cells nri = 1948, nrj = 22927 Try 63309box_margin = 3t overlap: Neighborsearching with a cut-off of 3 Table routines are used for coulomb: FALSE Tabl

[gmx-users] sulfate ion

Hi all I want to know about the ability of GROMACS to simulate sulfate in(SO4 (2-)), Do we can have the ion in our simulation using GROMACS? Thanks alot Saly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 213

experience, POL3 water model is a point polarizable > water model. > Point polarizable water models are not available in gromacs. > Gromacs uses shell model, i.e. charge attached on a spring to mimic the > stretching of the electronic cloud. > > So you have 3 solutions > a)

[gmx-users] Fwd: gmx-users Digest, Vol 84, Issue 217

> Message: 1 > Date: Wed, 27 Apr 2011 22:39:56 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] polarizable water models > To: Discussion list for GROMACS users > Message-ID: <4db80e9c.7010...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >

[gmx-users] Re: gmx-users Digest, Vol 84, Issue 217

> Message: 1 > Date: Wed, 27 Apr 2011 22:39:56 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] polarizable water models > To: Discussion list for GROMACS users > Message-ID: <4db80e9c.7010...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >

[gmx-users] sulfate ion

Hi all I want to know about the ability of GROMACS to simulate sulfate in(SO4 (2-)), Do we can have the ion in our simulation using GROMACS? Thanks alot Saly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] Re: gmx-users Digest, Vol 84, Issue 213

experience, POL3 water model is a point polarizable > water model. > Point polarizable water models are not available in gromacs. > Gromacs uses shell model, i.e. charge attached on a spring to mimic the > stretching of the electronic cloud. > > So you have 3 solutions > a)

[gmx-users] POL3 water model

Hi all I want to simulate using GROMACS.Before I used LAMMPS but it has not polarizable water models. Therefore I want to use GROMACS. I need .itp and .mdp files of POL3 water model. Do you have the files. Would you please help me. Thanks alot for your time and attention Regards Saly -- gm