[gmx-users] OPLS with Water models

Hi, This has been a long discussed question. But I am still not so clear after reading some posts and papers. What model should be used for OPLS-AA force field? Any consideration for the choice? Is SPC/E a good one? Michael shirts has said in http://lists.gromacs.org/pipermail/gmx-users/2002-July

Re: [gmx-users] OPLS with Water models

gt; Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: > Hi, > > This has been a long discussed question. But I am still not so clear > after reading some posts and papers. > What model should be used for OPLS-AA force field? Any consideration for &g

[gmx-users] CHARMM -> gromacs epsilon and sigma conversiion

eps(charmm)*4.184=epsilon(Gromacs) 0.15*4.184=0.6276 Rmin/2(Charmm)*2/(2^1/6)=sigma(Gromacs) 2.27*2/(2^(1/6))=0.404468(nm) Cheers, Jianhui Date: Fri, 24 Sep 2010 15:55:44 +0200 From: "ABEL Stephane 175950" Subject: [gmx-users] CHARMM -> gromacs epsilon and sigma conversiion factors To:

[gmx-users] Job crash: checkpoint file

Dear GMX users, I am running a replica simulation and the job crashed with the following message: File input/output error: Cannot rename checkpoint file; maybe you are out of quota? >From the mailling list, I see this might be a permission problem. However, I checked the file permission and noth

[gmx-users] electron density

Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I am using a CHARMM force field and the CHARMM version of TIP3P water. A

Re: [gmx-users] electron density

Date: Fri, 31 Dec 2010 19:08:50 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users Message-ID: <4d1e7092.7060...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: > Hi gmx us

Re: [gmx-users] electron density

Discussion list for GROMACS users Message-ID: <4d1f78ed.5070...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: > Date: Fri, 31 Dec 2010 19:08:50 -0500 > From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> > Subject: Re: [gm

[gmx-users] ACPYPE download

Hi there, I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein to GMX. The mailling list showed that ACPYPE should do the work. However, I can not get the program following the instructions on the wiki page. Is there anyone who has successful experience using ACPYPE and wou

Re: [gmx-users] ACPYPE download

harset=ISO-8859-1; format=flowed On 17/01/2011 5:05 AM, Jianhui Tian wrote: > Hi there, > > I am trying to convert a AMBER XLEaP generated topology file of > Glycoprotein to GMX. The mailling list showed that ACPYPE should do > the work. However, I can not get the program following

Re: [gmx-users] ACPYPE download

like in this >example: ./acpype.py -p file.top -x file.crd > > good luck, > Igor Marques > > > On Mon, Jan 17, 2011 at 6:37 PM, Jianhui Tian wrote: > >> I did find this page and followed the instructions. But I can not download >> it. >> >> JH

[gmx-users] Large fullerene ball simulations

Hi, I want to do some simulation about large fullerene balls. I searched the website and searched the mailing list. The largest fullerene ball I can get is C2160. But I want some larger ones like C3840 or so. Does anyone have any information about the coordinates and topology of large fullerene ba

[gmx-users] multiple processor running of gromacs-4.0.4

Hi, I have a small system of fullerene ball with waters. I want to simulation the system without pbc and pme, treating the coulomb and vdw without cutoff. The system can be run on single processor. But when I try to run it with multiple processors, it can't proceed. I am including the error messag

Re: [gmx-users] multiple processor running of gromacs-4.0.4

works on single node. Using cutoff for electrostatics and vdw with pbc and pme, the system can run on parallel. Thanks for the clarifications. Jianhui Jianhui Tian wrote: > Hi, > > I have a small system of fullerene ball with waters. I want to > simulation the system without pbc and pm

[gmx-users] Re: trjcat -demux problem

I solved the problem. The command that works is: trjcat -f md00.xtc md01.xtc ... md0N.xtc -o out00.xtc out01.xtc ... out0N.xtc -s replica_index.xvg Jianhui Date: Tue, 03 Nov 2009 10:24:12 -0500 From: "Justin A. Lemkul" Subject: [gmx-users] Re: trjcat -demux problem To: Jianhui Tian

[gmx-users] Error problem in free energy calculation

Hi, I have been trying to follow the tutorial http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial by David Mobley to reproduce the solvation energy for methane in water. I followed the instructions and got the solvation energy in good agreement with the answer in the tutorial.

[gmx-users] carbohydrate parameters in ffG53a6

Hi, I want to do some simulations about carbohydrates and glycolipid. In the ffG53a6.rtp file, I just see limited parameters for carbohydrate, like monosaccharide Glucose, Mannose and Galactose. What parameters can be used for others like arabinose? Also, is there any parameters available in the G

Re: [gmx-users] carbohydrate parameters in ffG53a6

ou are collected from the PRODRG. Hope this will help you. Regards... Parichita... Parichita Mazumder Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. --- On Wed, 18/8/10, Jianhui Tian wrote: From: Jianh

Re: [gmx-users] carbohydrate parameters in ffG53a6

on? Thanks. Jianhui Date: Wed, 18 Aug 2010 12:45:15 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 To: Discussion list for GROMACS users Message-ID: <4c6c0e1b.1020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

[gmx-users] dihedral function type 9 in rtp file

Hi, In the rtp file of Gromacs version 4.5-beta3, the dihedral function type for proper dihedrals is 9. However, I can't find any documentation about the function form of this function type. Also, you can add multiple dihedral potentials for one dihedral term explicitly in the rtp file. The term i

RE: [gmx-users] dihedral function type 9 in rtp file

Thanks Dallas. Forgot to search the mailing list this time. Jianhui Date: Thu, 26 Aug 2010 08:39:17 +1000 From: Dallas Warren Subject: RE: [gmx-users] dihedral function type 9 in rtp file To: Discussion list for GROMACS users Message-ID: < 39d19992d8a3804b8c801976acb4596247e...@prk-exch-

[gmx-users] CHARMM c36 to Gromacs

Hi, Gromacs 4.5-beta3 explicitly include the CHARMM c27 force field but not the c36 force field. Have anyone done any work to transfer the CHARMM c36 force field to Gromacs? Dr. Mark James Abraham has written a perl script to do the charmm_to_gromacs transfer, however that only works for the c27 w

[gmx-users] Problem after tranferred CHARMM c36 to Gromacs

Dear GMX users, I am interested in using CHARMM c36 force field in Gromacs. I wrote a script to generate the ffcharmmbon.itp, ffcharmmnb.itp and molecule.itp file. After that, I compared the energy terms from Gromacs and NAMD. The bond, angle, dihedral, improper and electrostatic energy terms all

[gmx-users] Problem after tranferred CHARMM c36 to Gromacs

Previously in gromacs, if you use Ryckaert-Bellemans type dihedrals, you must erase the 1-4 pairs. Now for 4.5-beta3 dihedral function type 9, how do you deal with the 1-4 pairs? Thanks. JH -- Forwarded message -- From: Jianhui Tian Date: Fri, Sep 3, 2010 at 10:17 AM Subject

[gmx-users] Questions about water in Gromacs

Dear gmx-users:   I am now studying a reverse micelle system using Gromacs. The system is like this: Isooctane outside, AOT reverse micelle in the center and water core inside the reverse micelle. I didn't use standard Gromacs force field, instead I am using a force field transferred from CHARMM fo

Re: [gmx-users] Questions about water in Gromacs

Hi,   Thank you for the suggestions. The water numbers should be fine. Becuase I can run the same system in AMBER ok. I have done minimization. And the system explodes during the equilibrium process.   I compared the energy of different component between AMBER and Gromacs. For all these components,

[gmx-users] Coulomb 1-4 interactions

Hi gmx-users:   I am running a comparison between AMBER and Gromacs for a AOT system. First I created the AMBER force field and then transformed it to Gromacs force field. I did 1 step of MD respectively in AMBER and Gromacs with the same configuration. All the energy terms including bond, angle, d

[gmx-users] Fatal error: Shake block crossing node boundaries

Hi GMX-Users, I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _ splitting topology... Walking down the molecule graph to make shake-blocks There are 24390 charge group b

[gmx-users] shake-block problem

Hi GMX-Users,  Does anyone have any idea about the problem? Thanks a lot in advance. I got an error message when using gromacs on 2 processors on the same computer.The error message is like this:_splitting topology... Walking down the

[gmx-users] RE: shake block problem

Hi GMX-Users, Does anyone have any idea about the problem? Thanks a lot in advance. I got an error message when using gromacs on 2 processors on the same computer. The error message is like this: _ splitting topology... Walking down