Re: [gmx-users] genion without stdin

On 2/13/20 5:59 AM, Christian Blau wrote: Hello Matthias, yes, if you use an indexfile with exactly one index group inside, this index group will be automatically picked. (like [ solvent ] 1001 1002 1003 1004 1005 1006 1007 1008 1009  ... and nothing else It's even easier than

Re: [gmx-users] genion without stdin

Hello Matthias, yes, if you use an indexfile with exactly one index group inside, this index group will be automatically picked. (like [ solvent ] 1001 1002 1003 1004 1005 1006 1007 1008 1009  ... and nothing else Best, Christian On 2020-02-13 11:49, Urban, Matthias wrote: Hello

[gmx-users] genion without stdin

Hello mailinglist, is there a way to prevent "gmx genion" from expecting input via stdin? I am using gromacs v2020 with gmxapi. Thanks in advance. Cheers, Matthias -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] genion problem with topology

On 7/3/18 1:47 PM, gangotri dey wrote: Dear all, I have replaced one water molecule in the solvent with a Cl atom using genion. My syntax is as follows: gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1 -nname CL I have generated the ions.tpr using the ion.mdp file as

Re: [gmx-users] genion problem with topology

What forcefield are you using? Check if CL is defined in your forcefield (it's probably not, which is why you are getting the error). Each type under [ molecules ] must have a corresponding [ moleculetype ] section defined somewhere in your forcefield files. On 3 July 2018 at 18:47, gangotri dey

[gmx-users] genion problem with topology

Dear all, I have replaced one water molecule in the solvent with a Cl atom using genion. My syntax is as follows: gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1 -nname CL I have generated the ions.tpr using the ion.mdp file as in the tutorial from Bevan group. I see that

Re: [gmx-users] Genion

/ | Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] From: "Mark Abraham" <mark.j.abra...@gmail.com> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, June 22, 2017 2:29:54 PM Subject: Re: [gmx-users] Genion Hi, The

Re: [gmx-users] Genion

/ | Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, June 22, 2017 2:29:40 PM Subject: Re: [gmx-users] Genion On 6/22/1

Re: [gmx-users] Genion

ttp://www.phap.no/ | FAP ] > > > > From: "Justin Lemkul" <jalem...@vt.edu> > To: "gmx-users" <gmx-us...@gromacs.org> > Sent: Thursday, June 22, 2017 2:21:17 PM > Subject: Re: [gmx-users] Genion > > On 6/22/17 8:14 AM, Sergio Manzetti

Re: [gmx-users] Genion

On 6/22/17 8:22 AM, Sergio Manzetti wrote: Thanks, Worked out. Now I got a note saying: NOTE 1 [file em.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme

Re: [gmx-users] Genion

lem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, June 22, 2017 2:21:17 PM Subject: Re: [gmx-users] Genion On 6/22/17 8:14 AM, Sergio Manzetti wrote: > OK, now I treied writing Na Cl and not NA and CL and get: > This is what you did before, so na

Re: [gmx-users] Genion

t;gmx-us...@gromacs.org> Sent: Thursday, June 22, 2017 2:09:02 PM Subject: Re: [gmx-users] Genion On 6/22/17 7:30 AM, Sergio Manzetti wrote: Hi, the procedure as defined by Juistin worked out well. However, a new problem has occurred. At m

Re: [gmx-users] Genion

emkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Thursday, June 22, 2017 2:09:02 PM Subject: Re: [gmx-users] Genion On 6/22/17 7:30 AM, Sergio Manzetti wrote: > Hi, the procedure as defined by Juistin worked out well. However, a ne

Re: [gmx-users] Genion

On 6/22/17 7:30 AM, Sergio Manzetti wrote: Hi, the procedure as defined by Juistin worked out well. However, a new problem has occurred. At mdrun for the minimization, I get: --- Program gmx mdrun, VERSION 5.1.2 Source code file:

Re: [gmx-users] Genion

ot;gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, June 21, 2017 4:53:59 PM Subject: Re: [gmx-users] Genion On 6/21/17 10:45 AM, Sergio Manzetti wrote: > Hi Justin, the sequence was: > > gmx editconf > > gmx solvate > > gmx grompp -f em -c dna_sol

Re: [gmx-users] Genion

21, 2017 4:53:59 PM Subject: Re: [gmx-users] Genion On 6/21/17 10:45 AM, Sergio Manzetti wrote: > Hi Justin, the sequence was: > > gmx editconf > > gmx solvate > > gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr > > gmx genion -s d

Re: [gmx-users] Genion

s.org> Sent: Wednesday, June 21, 2017 4:44:16 PM Subject: Re: [gmx-users] Genion On 6/21/17 10:30 AM, Sergio Manzetti wrote: > Hello, genion worked, and grompp was used to run the output conf from genion. > Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no

Re: [gmx-users] Genion

On 6/21/17 10:45 AM, Sergio Manzetti wrote: Hi Justin, the sequence was: gmx editconf gmx solvate gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL then: gmx grompp -f

Re: [gmx-users] Genion

On 6/21/17 10:30 AM, Sergio Manzetti wrote: Hello, genion worked, and grompp was used to run the output conf from genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no longer contains the Na Cl ions added to the system. When setting up the simulation, the input

[gmx-users] Genion

Hello, genion worked, and grompp was used to run the output conf from genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no longer contains the Na Cl ions added to the system. When setting up the simulation, the input confout.gro has no Na Cl ions, and the

Re: [gmx-users] genion -conc give the wrong number of multi-valent counter ion

Hi, In general, run "gmx help tool" to see how the tool should be run, here to see that there's an option for you to choose a non-default charge Mark On Fri, 16 Jun 2017 14:21 Justin Lemkul wrote: > > > On 6/16/17 7:14 AM, Quyen V. Vu wrote: > > Dear GMX developer, > > I

Re: [gmx-users] genion -conc give the wrong number of multi-valent counter ion

On 6/16/17 7:14 AM, Quyen V. Vu wrote: Dear GMX developer, I don't know this mailing list is suitable for posting issue or not, if not- forgive me. I want to report about gmx genion module If i want to add concentration of salt by -conc option, it just correct for monovalent salt (eg. NACL).

[gmx-users] genion -conc give the wrong number of multi-valent counter ion

Dear GMX developer, I don't know this mailing list is suitable for posting issue or not, if not- forgive me. I want to report about gmx genion module If i want to add concentration of salt by -conc option, it just correct for monovalent salt (eg. NACL). For multivalent salt(MGCL2), if I use

Re: [gmx-users] Genion error

Thank you very much Justin. It is good now. Best,Mohammad From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Monday, 29 May 2017, 23:40:06 Subject: Re: [gmx-users] Genion error On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote: > Thank you Justin. Here is

Re: [gmx-users] Genion error

in the archive. Run the topology through dos2unix and always make sure to use a plain text editor. See if that works. -Justin Kind regards,Mohammad From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Monday, 29 May 2017, 0:21:10 Subject: Re: [gmx-users] Genion

Re: [gmx-users] Genion error

gmx-us...@gromacs.org Sent: Monday, 29 May 2017, 0:21:10 Subject: Re: [gmx-users] Genion error On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote: > Hi All, when I wanted to add ions to the system, I got this error: > Fatal error:No line with moleculetype 'SOL' found the [ molecul

Re: [gmx-users] Genion error

On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote: Hi All, when I wanted to add ions to the system, I got this error: Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of file 'gr.top'For more information and tips for troubleshooting, please check the GROMACSwebsite

[gmx-users] Genion error

Hi All, when I wanted to add ions to the system, I got this error: Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of file 'gr.top'For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors

Re: [gmx-users] genion command

On 5/16/17 12:55 AM, Saumyak Mukherjee wrote: Hello Diana, You may try using the -conc flag in genion program to specify your salt concentration, along with -nname and -pname flags. The -nname and -pname options are irrelevant here. If there are fewer than 1000 waters in the system, I

Re: [gmx-users] genion command

Hello Diana, You may try using the -conc flag in genion program to specify your salt concentration, along with -nname and -pname flags. Best wishes, Saumyak On 16 May 2017 at 10:18, diana p wrote: > Dear gmx users, > I want to simulate 0.6M CaCL2 aqueous solution. To add

[gmx-users] genion command

Dear gmx users, I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use genion command and add 720 CL and 360 Ca ions respectively to the system of pure 12568 water molecules.But on running the command genion I get error message: Program genion, VERSION 4.6.5 Source code file:

Re: [gmx-users] genion

On 8/15/16 4:11 AM, f.namazi...@sci.ui.ac.ir wrote: Hi every body; Why we should neutralise net charge of the simulation system? To properly answer your question, we must approach it with a bit more nuance. One typically neutralizes the net charge of a condensed-phase system for two

Re: [gmx-users] genion

Depends on the simulation but in general, most of the biological systems occur at natural pH which around is 7.4, So mimicking the exact biological system we are neutralising the system. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] genion

Hi Farzaneh, If I am not entirely wrong; Otherwise, the tiny amount of charge in a single box would be huge in the calculation because of PBC(periodic boundary condition) and a coulomb explosion would happen. Cheers, Alex On Mon, Aug 15, 2016 at 10:11 AM, wrote: > Hi

[gmx-users] genion

Hi every body; Why we should neutralise net charge of the simulation system? Regards. Farzaneh -- 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

Re: [gmx-users] genion with Na or Ca

Thank you for your useful replies. Turgay 2016-01-12 23:38 GMT+02:00 VITALY V. CHABAN : > Ca(2+) will block one of your binding sites, if you care. > > > > > > On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak > wrote: > > > Hi all, > > > > > > I have

Re: [gmx-users] genion with Na or Ca

Ca(2+) will block one of your binding sites, if you care. On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak wrote: > Hi all, > > > I have a quick question about neutralizing the system. I have a solvated > system that contains a charged protein of -2q. Is there a

Re: [gmx-users] genion with Na or Ca

edu> Sent: Tuesday, January 12, 2016 7:41 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] genion with Na or Ca On 1/12/16 3:19 AM, Turgay Cakmak wrote: > Hi all, > > > I have a quick question about neutralizing the system. I have a solvated > system that contains a charged prote

Re: [gmx-users] genion with Na or Ca

On 1/12/16 3:19 AM, Turgay Cakmak wrote: Hi all, I have a quick question about neutralizing the system. I have a solvated system that contains a charged protein of -2q. Is there a major difference betwen adding 2 Na ions and a single Ca ion to neutralize the system (using genion)? For

[gmx-users] genion problem

Dear all I want to use bromide for neutralize my system. I wrote genion -s ions.tpr -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and I did not use K but in all cases my output was boron and I did

Re: [gmx-users] genion problem

On 10/5/15 2:26 AM, Golnaz Roudsari wrote: Dear all I want to use bromide for neutralize my system. I wrote genion -s ions.tpr -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and I did not use K

Re: [gmx-users] genion error sol not continuous

Hi Justin, Thanks for your email. I have modified it and the topology looks fine to me or at least I can't see any problem with it but still genion does not like it? Would please have a look? https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing

[gmx-users] genion question

Hi Dear Gromacs Users, I have a doubt , if i need a electrolyte concentration of 150mM of ions of NA and CL the right comand is genion -s file.tpr -o topol.top -nname CL -pname NA -neutral -conc 0.150 -o out.gro ? thanks in advance -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] genion question

On 7/23/14, 5:18 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote: Hi Dear Gromacs Users, I have a doubt , if i need a electrolyte concentration of 150mM of ions of NA and CL the right comand is genion -s file.tpr -o topol.top -nname CL -pname NA -neutral -conc 0.150 -o out.gro ? Yes. You can

Re: [gmx-users] genion

If you want a simulation w/o Zinc as a control then build a new system/pdb w/o it (just delete the Zn line) rather than doing something exotic like turning off its charge. Turning off charges (and van der Waals parameters) is an approach more suitable for alchemical calculations

[gmx-users] genion

dear users i studied on amyloid beta peptide with zinc cation and i choosed 1ze9 as my pdb file can i assume Zn without charge in protein simulation alone, or i have to using the amyloid beta peptide alone as pdb for instance,1iyt??? best wishes -- Gromacs Users mailing list * Please search the

Re: [gmx-users] genion

On 3/16/14, 9:49 AM, Andrew Bostick wrote: Dear Kalyan Thanks for your reply I want to use Zn2+ ions with my protein. There is Zn2+ ions in atomtypes.atp file of opls force field. But there is not Zn2+ ions in ions.itp file of of opls force field. Based on your answer, now, I can not use

[gmx-users] genion

Dear gromacs users In genion tool of gromacs, there are only Na and Cl ions. I want to add Zn2+ ions to my system. How to add these ions with special concentration? Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Genion command not working

Thank you very much your reply its working fine if i decrease distance thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/Genion-command-not-working-tp5010776p5014007.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing