[gmx-users] How to specify conection between 2 molecule in the top file?

Hi everyone, I have a question regarding a forcefield build. Is there a way to specify in the topology file how to bond two molecules one to another? So this thing, a halfaring + carboxyl on the left is one molecule and similar thing on the right is the other molecule. But I need to bond carbons

Re: [gmx-users] How to specify conection between 2 molecule in the top file?

best and from now on my post will contain only the utmost reverance. Would you be kind to clearify the second part of may question? Namely, could "+" and "-" signs, mentioned in the manual and used in the rtp files be helpfull to me in this case? Yours Gratefully, Frankie M

[gmx-users] (no subject)

Hi guys, My first question is with regards to the size relationship between rlist and rvdw/rcoulomb, and consequently the meaning of rlist. I found an excellent question on this exact same subject posted couple of years ago, but I couldn't find the answer to it. I copy parts of the question here

[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

Hi guys, My first question is with regards to the size relationship between rlist and rvdw/rcoulomb, and consequently the meaning of rlist. I found an excellent question on this exact same subject posted couple of years ago, but I couldn't find the answer to it. I copy parts of the question here

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

So if you box size is 5 (as you say) and your cut-off is 1, then you should not get an error. So one of the two things is wrong. Maybe you made a pdb file with box 5? pdb is in Angstrom, while Gromacs uses nm, so there is a conversion factor of 0.1. Berk. That's what it was. Thanks a bunch. A f

Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units

I think that what you want is inconsistent. If you want dispersion correction this means that in principle you do not want cut-off's. Berk, you are right: I don't want any cutoffs, I am trying to avoid them. But I thought the way Gromacs works is, if you don't choose one, you get assigned the d

[gmx-users] 8MB CPU cache vs 4MB CPU cache: large difference in performance?

Hi, I am about to purchase several units with Intel's quadcore q6600 processors. Since about 80% of our work is done with Gromacs, I figured this list is a place to ask performance questions. I was wondering if there would be any significant benefit in having a q6600 processor with 8MBof L2 cache

[gmx-users] 8MB CPU cache vs 4MB CPU cache: large differen

Hi, I am about to purchase several units with Intel's quadcore q6600 processors. Since about 80% of our work is done with Gromacs, I figured this list is a place to ask performance questions. I was wondering if there would be any significant benefit in having a q6600 processor with 8MB of L2 cac

[gmx-users] Re: 8MB CPU cache vs 4MB CPU cache: large difference in performance?

Upps, sorry. I should have searched the list before asking the question ( http://www.gromacs.org/index.php?option=com_wrapper&Itemid=165 ). Still, the numbers in this thread are from 2004, so...is the answer still the same? Thnx, F. On 9/8/07, Frankie Montenegro <[EMAIL PROTECTED]

[gmx-users] Surface Accessible Volume with g_sas: possible or not?

Hi guys, I am trying to compute molecular volume for protein. I found this when searching the user's list: :This following excerpt was on the gmx-revision list in July. You probably need the CVS version of 3.3 to take advantage of this option: I've used it myself, with that version. Seems to wor

[gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water molecules, two tools are mentioned on

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

On 9/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > That sounds difficult because computing volume is difficult. We should > write a better program for this, but the problem lies in definition: > where does one water molecule stop

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

On 9/11/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Hi again guys, > > > > Few more questions: > > > > 1. I would like to calculate compressibility of the protein+water > > system, but separating it into bulk water, h

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Thanks, Frankie _

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

/mol.K F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > I am not sure what I'm missing here. I just ran an example from > /tutor/water and got even worse > number for specific heat, around 12.5 J/mol.K. Sure, it was with > Berendsen T-coupling, no shifted VdW, but

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

David, I didn't realize what the nmol option does, thanks for the tip. But the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk as I type this). BTW why ndf 6 and not 3? For rotation? On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Monte

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is correct for ndf? I am running ffgmx force field and all bonds constrained spc water. F. On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > David, > I didn't realize what the nmol option does, thanks

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

l 216 -ndf 9; Cv=55J/mol.K (close) g_energy -nmol 216 -ndf 10; Cv=88J/mol.K (even closer) Not that I can justify those ndf values though. F. On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Correction: the number is -706.4J/mol.K (negative)

[gmx-users] To deshuffle or not to deshuffle, that is a question.

Hi guys, A stupid question: I got myself confused with this shuffling/deshuffling thing, which I shouldn't have been doing with protein in the first place. So this are my steps, done on the same 4 nodes, please tell me whether I was supposed to do any deshuffling of .trr and .gro files, and fol

Re: [gmx-users] To deshuffle or not to deshuffle, that is a question.

and should be avaialbe in next gromacs version. > > > > Stéphane > > > Instead, -shuffle and -sort will all disappear in the next version. I > encourage Frankie to benchmark the speed-up ratio, especially it is not > a membrane system. I know that people would not use

[gmx-users] Designing a topology file: bonded/non-bonded mess

Hi all, I am hoping someone could give me advice regarding a topology file design. I am trying to implement a forcefield for an organic crystal with 30 atoms at each site (therefore, 30 atom basis). Sites are connected by an aromatic ring. The forcefield I am trying to implement does not treat r

Re: [gmx-users] Designing a topology file: bonded/non-bonded mess

Wow, I didn't realize you guys in Europe work 24/7 too. On Sunday morning nonetheless :-) On 10/14/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > question: are there chemical bonds between "molecules" (which you seem > to imply by stating the sites are connected by an aromatic ring). If > t

[gmx-users] bonded Buckingham interaction

Hi everyone, I am trying to implement a force field for a metalorganic crystal. In this FF, there is a Buckingham interaction between two neighboring atoms, O and Zn. This interaction exists only for atoms on the same crystal site. So, bonded Buckingham interaction added in [ pairs ] would be a

Re: [gmx-users] bonded Buckingham interaction

, it would be much easier to use nonbonded Buckingham: is there no way I could set up rvdw at 5A while keeping rcoulomb at 10A? Thanks, F. On Nov 9, 2007 4:14 AM, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Hi everyone, > > > > I am tr

[gmx-users] Q's about adding bonded interaction

Hi everyone, *I have posted these few questions on the developers list few days ago but didn't get any feedback. I'd really appreciate some input, I am quite lost in gromacs (not so small) source tree.* I am trying to add a two-body bonded interaction, following a "list of files to modify", given