Re: [gmx-users] g_sans

r > of the software is a colleague in my group). > > Roland > > > On Tue, Dec 18, 2012 at 4:10 PM, Justin Lemkul wrote: > > > > > > > On 12/18/12 3:59 PM, XUEMING TANG wrote: > > > Hi there > > > > > > I searched through the websi

Re: [gmx-users] g_sans

Hi Justin Thank you for this information. I am looking forward for the code to be ready! Happy holidays! Best! Xueming On Tue, Dec 18, 2012 at 4:10 PM, Justin Lemkul wrote: > > > On 12/18/12 3:59 PM, XUEMING TANG wrote: > >> Hi there >> >> I searched through th

Re: [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)

Got it! Thank you, Justin! Best! Xueming On Wed, Nov 14, 2012 at 1:37 PM, Justin Lemkul wrote: > > > On 11/14/12 1:14 PM, XUEMING TANG wrote: > >> Hi Stephane >> >> So if I could use CHARMM dihedral potential in charmm force field, I donot >> need to cons

Re: [gmx-users] Ryckeat-Bellemans Potential in Charmm forcefield (XUEMING TANG)

Hi Stephane So if I could use CHARMM dihedral potential in charmm force field, I donot need to consider the RB potential? I used to use GROMOS forcefield that need to consider RB. I recently tried CHARMM and wondered if I should use RB potential in CHARMM or not. Best! Xueming On Wed, Nov 14, 20

Re: [gmx-users] forcefield.itp file for gromos45a3 and oplsaa

Got it, Thank you, Mark! Best! Xueming On Wed, Jan 4, 2012 at 1:18 AM, Mark Abraham wrote: > On 4/01/2012 4:43 PM, XUEMING TANG wrote: > >> Hello >> >> I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) and >> also in Gromos (C6 and C12) force

[gmx-users] forcefield.itp file for gromos45a3 and oplsaa

Hello I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) and also in Gromos (C6 and C12) forcefield for comparison. The original ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the original ffnonbonded.itp file in gromos**.ff listed all the pair potentials.

Re: [gmx-users] Topology dihedral or improper dihedral

be the best choice for the topology file. Or any choices could be right and I have to try which one provide consistent results with experiment by trial? Best! Xueming On Sun, Nov 13, 2011 at 9:57 AM, lina wrote: > On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG > wrote: > > Hi there

[gmx-users] Topology dihedral or improper dihedral

Hi there I am trying to build up a topology file for a tetra nitrogen molecule using Gromos UA and OPLS UA force field. Following are the molecules. 1. for C | A. C-C-C-C-C-C-C-N-C and |

Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

Got it (cool :)), Thank you!!! Best! Xueming On Wed, Jun 8, 2011 at 1:15 PM, Justin A. Lemkul wrote: > > > XUEMING TANG wrote: > >> Hi Justin >> >> Sorry I did not explain clearly. I apply position restraint to the head >> group of surfactant molecules and

Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

you and have a nice day :P Best! Xueming On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul wrote: > > > XUEMING TANG wrote: > >> Hi there >> >> I put a SDS Spherical micelle in solution and want to apply position >> restraint before mdrun. Here I have

[gmx-users] a question about position restraint time for long alkyl chain molecules

Hi there I put a SDS Spherical micelle in solution and want to apply position restraint before mdrun. Here I have a question: For macromolecules like micelles, should the position restraint apply to not only the water molecules (and ions) but also to the surfactant molecules in the micelle? If it

[gmx-users] amide partial charges in G56A3

Hi there The amide partial charges in the share folder of gromacs G56A3ff is as following H H: +0.280 N: -0.280 | C: -0.380 O: -0.380 C-N-C-C other C : 0.000 " O I guess all protein people use pa

[gmx-users] amide partial charges

Hi May I ask if anyone know a good reference for partial charges of "-CH2-NH-CO-CH2-CH2"(amide)? I plan to use gromos 53A6 force field. I searched the internet quite a while but not sure what is the best. I will be appreciated if you could recommend one with the reference paper. Thank you in advan

[gmx-users] Comparing ff in Topology file by PRODRG and gromos G45a3

Hi there This is maybe an old question. I want to ask a general procedure of generate topology file with gromo96 force field by Dundee Prodrg. Take SDS for an example, I want to use gromos96 G45a3 forcefield. After the file is generated by dundee, I compare the forcefield parameter of G45a3 with w

Re: [gmx-users] Units of k1 in the pulling code

Dear Chris: Thank you very much for it! Best! Xueming On Thu, Aug 12, 2010 at 5:33 PM, wrote: > Dear Xueming: > > the word "mol" is short form for "mole" > > http://en.wikipedia.org/wiki/Mole_%28unit%29 > > In the pull code context, it refers to moles of the pulled group. > > The force is not

Re: [gmx-users] Units of k1 in the pulling code

Dear Berk: Thank you so much for the clarification!!! It is so helpful! Best! Xueming On Fri, Aug 13, 2010 at 4:13 AM, Berk Hess wrote: > > > > Date: Thu, 12 Aug 2010 17:33:09 -0400 > > From: chris.ne...@utoronto.ca > > To: gmx-users@gromacs.org > > Subject: [gmx-users] Units of k1 in the pull

[gmx-users] Units of k1 in the pulling code

Hi there The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a cluster, the "/mol" in the units of force means per atom in the cluster, or single molecule composed of several atoms? Sorry, I don't know the default value of mol in gromacs. Does that mean per molecule? Besides, the for

Re: [gmx-users] how to position restraint COM of clusters?

Thank you, Justin. Your answer saved my time from further searching the web. On Fri, May 28, 2010 at 1:16 PM, Justin A. Lemkul wrote: > > > XUEMING TANG wrote: > >> Hi >> I noticed a new position restraint com function of Gromacs (Implement new >> position rest

[gmx-users] Fwd: how to position restraint COM of clusters?

Hi I noticed a new position restraint com function of Gromacs (Implement new position restraints that restrain particles with respect to the center of mass of a group (e.g. for cluster simulations).) How can I get detailed mdp file set up for this function? Is it a pr.mdp or md.mdp with pull code?

[gmx-users] how to position restraint COM of clusters?

Hi I noticed a new position restraint com function of Gromacs (Implement new position restraints that restrain particles with respect to the center of mass of a group (e.g. for cluster simulations).) How can I get detailed mdp file set up for this function? Is it a pr.mdp or md.mdp with pull code?