[gmx-users] remove the atom clashes-reg

Hi Dear, I am doing simulation with three ligand so that I have applied deprecated force field to the system. I went through the reference which you cited to the following error. I understood the error that It could be a clashes. It wanted to remove atom clashes from my coordinate file, so Is th

[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

Dear all, We have tested more strange behavior of constraints from pull code for calculation of free energy differences small molecule on DOPC membrane and octanol slab. As I have reported previously, while the errors in free energy differences on DOPC were rather small, the errors on octanol were

Re: [gmx-users] remove the atom clashes-reg

On 31/08/2011 6:15 PM, ITHAYARAJA wrote: Hi Dear, I am doing simulation with three ligand so that I have applied deprecated force field to the system. That's a bad reason to choose a deprecated force field. I went through the reference which you cited to the following error. I understood th

[gmx-users] g_hbond

Hi Gromacs Users, I have calculated hydrogen bonds and collisions between my ligands and every single residue using g_hbond. Looking at the criteria adpoted by Gromacs I found impossible that number of hydrogen bonds were higher than number of collisions... And what is interesting in one of my res

Re: [gmx-users] g_hbond

Steven Neumann wrote: Hi Gromacs Users, I have calculated hydrogen bonds and collisions between my ligands and every single residue using g_hbond. Looking at the criteria adpoted by Gromacs I found impossible that number of hydrogen bonds were higher than number of collisions... And what i

Re: [gmx-users] g_hbond

On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Gromacs Users, >> I have calculated hydrogen bonds and collisions between my ligands and >> every single residue using g_hbond. Looking at the criteria adpoted by >> Gromacs I found impossible that numbe

Re: [gmx-users] g_hbond

Steven Neumann wrote: On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Hi Gromacs Users, I have calculated hydrogen bonds and collisions between my ligands and every single residue using g_hbond. Looking

Re: [gmx-users] g_hbond

Steven Neumann wrote: On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Hi Gromacs Users, I have calculated hydrogen bonds and collisions between my ligands and every single residue using g_hbond. Looking

Re: [gmx-users] g_hbond

On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Hi Gromacs Users, >> I have calculated hydrogen bonds and collisio

[gmx-users] pdb2gmx of nucleic acids with ffamber03 force field

Dear all, I am trying to pdb2gmx a a pdb file gcaa.pdb having nucleic acids using amber force field 03: pdb2gmx -ff amber03 -f gcaa.pdb -o rna.pdb -p rna.top -water tip3p I have two questions: 1. The ffamber03.rtp file specifies that O2 from should be O to be recognized by the rtp file. Whe

Re: [gmx-users] g_hbond

On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Hi Gromacs Users, >> I have calculated hydrogen bonds and collisio

Re: [gmx-users] g_hbond

Steven Neumann wrote: On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

Re: [gmx-users] pdb2gmx of nucleic acids with ffamber03 force field

MARIA ICIAR FRADES ALZUETA wrote: Dear all, I am trying to pdb2gmx a a pdb file gcaa.pdb having nucleic acids using amber force field 03: pdb2gmx -ff amber03 -f gcaa.pdb -o rna.pdb -p rna.top -water tip3p I have two questions: 1. The ffamber03.rtp file specifies that O2 from should be O to

Re: [gmx-users] g_hbond

Steven Neumann wrote: On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

[gmx-users] Free energy calculation question

Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent.  I have a question referring to your free energy tutorial.  You mentioned that decoupling of electrostatic interactions is linear and decoupling of vdW can vary.  Is this true for your case of methanol in water or for a

Re: [gmx-users] g_hbond

Thank you for clarification Justin!!! The Manual is not as clear as you :P Steven On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >>

Re: [gmx-users] g_hbond

One question for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a side chain. How about other amino acids and their maximum hbonds they can create? Steven On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann wrote: > Thank you for clarification Jus

Re: [gmx-users] g_hbond

Steven Neumann wrote: One question for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a side chain. How about other amino acids and their maximum hbonds they can create? Any OH or NH group is a donor, any lone pair is an acceptor (though

Re: [gmx-users] Free energy calculation question

Fabian Casteblanco wrote: Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent. I have a question referring to your free energy tutorial. You mentioned that decoupling of electrostatic interactions is linear and decoupling of vdW can vary. Is this true for your case

[gmx-users] Re: Free energy calculation question

Hello Justin, I'm looking at the dG vs Lambda plot that is an output from G_bar but on the Shirts et al paper that you included, the part where it talks about linearity, it is referring to dH/dLambda for electrostatic decoupling. So if I take the line formed by dGtotal vs Lambda from g_bar output

Re: [gmx-users] Re: Free energy calculation question

Fabian Casteblanco wrote: Hello Justin, I'm looking at the dG vs Lambda plot that is an output from G_bar but on the Shirts et al paper that you included, the part where it talks about linearity, it is referring to dH/dLambda for electrostatic decoupling. So if I take the line formed by dGtot

[gmx-users] Re: Free energy calculation question

Hello Justin, You mean that only for vdW decoupling, you would need to use soft-core potentials? I had soft -core potentials on for decoupling the electrostatic interactions (see below). What would I use in its place? Thanks again for your help! ;Production MD ;--

Re: [gmx-users] Re: Free energy calculation question

Fabian Casteblanco wrote: Hello Justin, You mean that only for vdW decoupling, you would need to use soft-core potentials? I had soft -core potentials on for decoupling the electrostatic interactions (see below). What would I use in its place? Thanks again for your help! You only need s

[gmx-users] Re: Free energy calculation question

Thanks Justin! On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco wrote: > Hello Justin, > > I'm calculating the free energy of a drug in an alcohol solvent.  I > have a question referring to your free energy tutorial.  You mentioned > that decoupling of electrostatic interactions is linear and

[gmx-users] doubt in deuterium order parameter

Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the

[gmx-users] order parameter

Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the –C

[gmx-users] which charge is used in gromacs program

Hi, ALL I have a question about the charge defined in the topology file. It seems to me that the charge for each atom apprears twice in different sections of the topology files. -- One is [ atomtypes ] ;n

Re: [gmx-users] which charge is used in gromacs program

GZ Zhang wrote: Hi, ALL I have a question about the charge defined in the topology file. It seems to me that the charge for each atom apprears twice in different sections of the topology files. -- O

[gmx-users] Re: which charge is used in gromacs program

> > Hi, ALL > >      I have a question about the charge defined in the topology file. >      It seems to me that the charge for each atom apprears twice in > different sections of the topology files. > -- >      One is > [

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000

Re: [gmx-users] Re: which charge is used in gromacs program

Dr. Vitaly V. Chaban wrote: Hi, ALL I have a question about the charge defined in the topology file. It seems to me that the charge for each atom apprears twice in different sections of the topology files. --

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Hideya Nakamura requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Hideya Accept invitation from Hideya Nakamura http://www.linkedin.com/e/-85v1n9-gs

Re: [gmx-users] Re: which charge is used in gromacs program

On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul wrote: > > > Dr. Vitaly V. Chaban wrote: >>> >>> Hi, ALL >>> >>>     I have a question about the charge defined in the topology file. >>>     It seems to me that the charge for each atom apprears twice in >>> different sections of the topology file

Re: [gmx-users] Re: which charge is used in gromacs program

On 1/09/2011 10:34 AM, Dr. Vitaly V. Chaban wrote: On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul wrote: Dr. Vitaly V. Chaban wrote: Hi, ALL I have a question about the charge defined in the topology file. It seems to me that the charge for each atom apprears twice in different

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.

[gmx-users] order parameter

Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC woul

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: > On 1/09/2011 10:20 AM, Itamar K

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different.

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes

[gmx-users] GROMACS 4.5.4 keep crashing all the time

Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may nee