[gmx-users] interaction force between Mg and Oxygens of phosphate, in CHARM36 force field

Hello Dears, I am using CHARM-36.ff for my simulation. I have Mg ions and ATP as hetero-atoms in my system (the Mg-ATP complex). I am trying to know about the amount of interaction force between Mg ions and phosphates of ATP that is already set in this force field. Could you please help me know

[gmx-users] -inter command

> Message: 1 > Date: Tue, 16 Jan 2018 08:30:10 +0100 > From: Jo?o Henriques > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] -inter command > Message-ID: >

[gmx-users] inter- and intra-molecular hbond analysis

Dear Gromacs users, Given a mixed bilayer composed of two lipids (type A and B), I would like to calculate: 1) "Intramolecular" h-bonds for a lipid type to see if part of lipid (NH3+ of PE) is interacting with some other part of itself (PO4- of the same lipid). 2) "intermolecular" hbonds

Re: [gmx-users] rlist- group scheme

Hi, There could be. But over what range does your table work correctly? What do you get when you have a two particle system at various displacements? Mark On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh wrote: > Dear Mark, > > Thank you, however, the problem occurs when

Re: [gmx-users] rlist- group scheme

Dear Mark, Thank you, however, the problem occurs when 'table' is used. For vdWtype=not-user the energies are OK and the same for both cases, as I mentioned. So I guess there should be something wrong in the way Gromacs interpolates the table with cutoffs and rlist. Best regards Best regards

[gmx-users] Best method for equilibrating lipid system (Amber parameters)

Dear Gromacs Community, I am trying to determine the most appropriate way to equilibrate my system which contains lipid, protein, and water. I built the system using CHARMM-GUI, but I used only the .pdb coordinates and instead I parameterized it with Amber using the Lipid17, ff14SB, and tip3p

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 85

Hi, If you want to engage in discussion, please change your settings so that you aren't receiving digests and replying to them, because that means you make it hard for all to know what you are replying about. Mark On Fri, Jan 19, 2018, 20:01 banijamali_fs wrote: > On

Re: [gmx-users] rlist- group scheme

Hi, With the group scheme, when you choose nstlist > 1 then you get a list of all the groups that satisfy rlist, whatever it is, and continue to use that list for the whole lifetime. If you chose rlist==rcoulomb, then rcoulomb is never considered again, because you chose to use an unbuffered

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 85

On 2018-01-19 16:25, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit >

Re: [gmx-users] Which files does "-cpi -append" need?

Hi, One could just avoid using -deffnm and avoid creating problems ;-) Or if the md_0_1 name reveals that what you want is each piece on its own, and to have to append manually later, use just -noappend and let mdrun generate md.part0001.log, energy.part0001.log etc for you. Mark On Fri, Jan

Re: [gmx-users] Electric Field

Dear Mark, Thank you. this is good I will study it. On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham wrote: > Hi, > > See section 6.7 of the 2018 reference manual for what is supported. > > MArk > > On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed wrote:

[gmx-users] Why gyration radius keep dropping?

Dear Gromacs, I am running MD at 500 K for my protein. I used this to analyse the gyration radius echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg I thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a

Re: [gmx-users] Which files does "-cpi -append" need?

On 1/19/18 11:53 AM, ZHANG Cheng wrote: Thank you very much Justin! Sorry I did not realise that. I will need to include an "except md_0_1.edr" in the deletion. But does it correct that I can delete all the log files? md_0_1.e md_0_1.o md_0_1.pe md_0_1.po Those are output from your

Re: [gmx-users] Which files does "-cpi -append" need?

Thank you very much Justin! Sorry I did not realise that. I will need to include an "except md_0_1.edr" in the deletion. But does it correct that I can delete all the log files? md_0_1.e md_0_1.o md_0_1.pe md_0_1.po -- Original -- From: "ZHANG

Re: [gmx-users] Which files does "-cpi -append" need?

On 1/19/18 11:45 AM, ZHANG Cheng wrote: Dear Gromacs, I run Gromacs on our cluster, and use this command to continue my run from last checkpoint. gmx mdrun -deffnm md_0_1 -cpi -append Each new run will generate four log files: md_0_1.e md_0_1.o md_0_1.pe md_0_1.po Gradually, I have

[gmx-users] Which files does "-cpi -append" need?

Dear Gromacs, I run Gromacs on our cluster, and use this command to continue my run from last checkpoint. gmx mdrun -deffnm md_0_1 -cpi -append Each new run will generate four log files: md_0_1.e md_0_1.o md_0_1.pe md_0_1.po Gradually, I have thousands of log files. So I used these

Re: [gmx-users] tilt angle for POPC

Thanks, I agree. I will do as you recommended. Cheers, Mohsen On Fri, Jan 19, 2018 at 9:23 AM, Justin Lemkul wrote: > > > On 1/19/18 11:16 AM, Mohsen Ramezanpour wrote: > >> On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul wrote: >> >> >>> On 1/18/18 1:28 PM,

Re: [gmx-users] tilt angle for POPC

On 1/19/18 11:16 AM, Mohsen Ramezanpour wrote: On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul wrote: On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: On 1/18/18 12:24 AM, Mohsen

Re: [gmx-users] Electric Field

Hi, See section 6.7 of the 2018 reference manual for what is supported. MArk On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed wrote: > Hello GROMACS users > I have looked through GROMACS user manual to understand the theory behind > applying external electric field but I did not

Re: [gmx-users] tilt angle for POPC

On Fri, Jan 19, 2018 at 5:55 AM, Justin Lemkul wrote: > > > On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: > >> Hi Justin, >> >> On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: >> >> >>> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: >>> >>> Dear Gromacs

[gmx-users] Electric Field

Hello GROMACS users I have looked through GROMACS user manual to understand the theory behind applying external electric field but I did not find any description. Also, I looked at the source code in sim_util.cpp file but found only the time-dependent electric field. My question does GROMACS

Re: [gmx-users] -inter command

On 1/19/18 7:25 AM, za...@tezu.ernet.in wrote: Message: 3 Date: Thu, 18 Jan 2018 07:39:39 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -inter command Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed...@vt.edu> Content-Type: text/plain;

[gmx-users] -inter command

> Message: 3 > Date: Thu, 18 Jan 2018 07:39:39 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] -inter command > Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 1/18/18

[gmx-users] rlist- group scheme

Hi, I run a simple example using Table,6,12 (for LJ) with vdW type= user. Then group scheme should be chosen. In results, I got different LJ energies when I set rlist=rcoulomb and rlist>rcoulomb (which is allowed in this scheme). I see in the manual that with group scheme that can be happen. But

Re: [gmx-users] tilt angle for POPC

On 1/18/18 2:44 PM, Mohsen Ramezanpour wrote: I did more tests and here are the conclusions for the pick mentioned earlier. The pick appears when the -binw gets smaller and smaller. For the default value of gangle (which is 1), one cannot detect such a pick and you will get a normal

Re: [gmx-users] tilt angle for POPC

On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote: Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution

Re: [gmx-users] Rupture force definition

On 1/19/18 12:52 AM, Rakesh Mishra wrote: Dear Justin Thanks for your explanation . Yes I am agree that it will depend on the k value and path direction. Let suppose we map the experimental spring constant and rate then it will be some how relevant for my study. My another query is the same

Re: [gmx-users] help with my errors (RAHUL SURESH)

On 1/19/18 7:09 AM, RAHUL SURESH wrote: On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs wrote: Hi there, 1. I'm working on MOF (metal organic framewoks) structures. I'd like to know that if in our topology file we get a decimal figure for the qtot, in which step we

Re: [gmx-users] help with my errors (RAHUL SURESH)

On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs wrote: > > Hi there, > > > > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to > > know that if in our topology file we get a decimal figure for the qtot, > > in which step we made a mistake? and how we

Re: [gmx-users] help with my errors (RAHUL SURESH)

> Hi there, > > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to > know that if in our topology file we get a decimal figure for the qtot, > in which step we made a mistake? and how we can rectify this? > > 2. Another question that I have is that when I want to run this

Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit

I see what you mean. I've also worked with methods that required modification/wrapping of specific (older) versions of gromacs. The amount of people that do this is however much lower than those running vanilla gromacs, so you should probably conserve your time and effort, unless there's a big

Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit

Hi James, Joao: Thanks for your reply. I know the 4.5.5 is a old version, but I found some useful paper used this version, and some of my work in graduate school is based on the method developed on this version. At the same time, my work is a stand-alone software application. I had a hard time

Re: [gmx-users] help with my errors

On Fri, Jan 19, 2018 at 2:12 PM, banijamali_fs wrote: > Hi there, > > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to > know that if in our topology file we get a decimal figure for the qtot, > in which step we made a mistake? and how we can

[gmx-users] help with my errors

Hi there, 1. I'm working on MOF (metal organic framewoks) structures. I'd like to know that if in our topology file we get a decimal figure for the qtot, in which step we made a mistake? and how we can rectify this? 2. Another question that I have is that when I want to run this command, gmx

Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit linux system

Exactly, that version is 7 years old or so. It's a good initiative nonetheless, just wished it offered a more recent version. J On Fri, Jan 19, 2018 at 6:08 AM, James Krieger wrote: > Why 4.5.5? > > On Thu, Jan 18, 2018 at 11:26 PM, 蕭毅 wrote: >