Re: [gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?

On 2010-10-22 00.49, Chih-Ying Lin wrote: Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not

RE: [gmx-users] CHARMM36 lipid bilayers

Hi, Another comment on your interaction settings. You did not mail if you are using shift or switch for vdw. But I guess that both probably don't match exactly what Charmm does. Since the switching range is so long and this is where a large part of the dispersion attraction acts, this might have

[gmx-users] hbond correlation function

Hi.. all I would like to calculate the hydrogen bond correlation function C(tau) for protein water hbonds and water-water hbonds. In the manual it is written that using g_hbonds one can calculate C(tau), however it does not say clearly how to calculate the C(tau) between different groups present

Re: [gmx-users] CHARMM36 lipid bilayers

Hi there, Tom, thanks for this hint, yes, that is an improvement. I am looking forward to your paper. Berk, I am using switch for vdw. Although for my taste switching from 0.8 to 1.2 was quite large, I used it because the charmm paper used these values. But I just realized that the implementation

Re: [gmx-users] hbond correlation function

Navjeet Ahalawat skrev 2010-10-22 10.46: Hi.. all I would like to calculate the hydrogen bond correlation function C(tau) for protein water hbonds and water-water hbonds. In the manual it is written that using g_hbonds one can calculate C(tau), however it does not say clearly how to calculate

Re: [gmx-users] CHARMM36 lipid bilayers

Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda paper where they show a decreased area per lipid (~63 A^2 to ~58 A^2) in the NAMD DPPC simulations (see the graph in the

Re: [gmx-users] RE: Gibbs free energy of binding

reading your idea: it seems to me I can't ignore entropy contribution because my simulation is at room tempreture. Really I couldn't understand what can I do! I am working at room tempreture and I want to estimate binding free energy(delta G),can I ignore entropy in this simulation and calculate

[gmx-users] genconf to insert small molecules triclinic unit cell

Hi, I have a strange problem when I try to insert small molecules into my cell using genconf. Here the cell is a crystalline metal-organic framework with lots of space for the molecules inside. The edges of the metal organic framework defined the pbcs. When I view the final structure,

Re: [gmx-users] CHARMM36 lipid bilayers

I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär Hi Sven, Yes I have tested values of rvdw-switch and (unlike in your test) have seen a large impact of the area per lipid. Indeed this can also be seen in the Klauda

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi Carsten, I've been thinking a bit about this issue, and for now a relatively easy fix would be to enable thread affinity when all cores on a machine are used. When fewer threads are turned on, I don't want to turn on thread affinity because any combination might either - interfere with

Re: [gmx-users] CHARMM36 lipid bilayers

Yes, I was surprised as well. It depends on the value of rvdw-switch. For some systems it can be 10 A^2, for others much smaller. Tom Pär Bjelkmar wrote: I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately? /Pär Hi Sven,

Re: [gmx-users] GPU slower than I7

Hi Renato, First of all, what you're seeing is pretty normal, especially that you have a CPU that is crossing the border of insane :) Why is it normal? The PME algorithms are just simply not very well not well suited for current GPU architectures. With an ill-suited algorithm you won't be able to

Re: [gmx-users] genconf to insert small molecules triclinic unit cell

Jennifer Williams wrote: Hi, I have a strange problem when I try to insert small molecules into my cell using genconf. Here the cell is a crystalline metal-organic framework with lots of space for the molecules inside. The edges of the metal organic framework defined the pbcs. When I

Re: [gmx-users] genconf to insert small molecules triclinic unit cell

Jennifer Williams wrote: Hi Justin, Thanks for the response (again!). I would be happy if genbox inserted molecules randomly (within the box defined by my .pdf file) but the output doesn't look random but subject to some strange (symmetry?)constraints which don't allow random insertions

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Thanks Justin, this explains everything. I've got #include my.ff/forcefield.itp line in my top file. My guess is that this is a matter of how the force field was #included in the .top file. For instance: #include my.ff/forcefield.itp will match $GMXLIB first, but #include

Re: [gmx-users] genconf to insert small molecules triclinic unit cell

Hi Justin, The .pdb I sent with my last e-mail was a result of trying to add 500 molecules. The max of 168 were added and then genconf couldn't add anymore despite the large vacant space. Trying to add more molecules to this .pdb won't work. This is what makes me think the space was

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

On Thu, Oct 21, 2010 at 14:28, Justin A. Lemkul jalem...@vt.edu wrote: My guess is that this is a matter of how the force field was #included in the .top file.  For instance: #include my.ff/forcefield.itp will match $GMXLIB first, but #include ./my.ff/forcefield.itp will match the

[gmx-users] Subject: basic questions about _FF_FORCEFIELD statement.....

Dear gmx-users I have some very basic questions about the following statements: #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no1.0 1.0 #include ffnonbonded.itp #include ffbonded.itp 1) What

Re: [gmx-users] genconf to insert small molecules triclinic unit cell

Jennifer Williams wrote: Hi Justin, The .pdb I sent with my last e-mail was a result of trying to add 500 molecules. The max of 168 were added and then genconf couldn't add anymore despite the large vacant space. Trying to add more molecules to this .pdb won't work. This is what makes me

Re: [gmx-users] Subject: basic questions about _FF_FORCEFIELD statement.....

Alberto Sergio Garay wrote: Dear gmx-users I have some very basic questions about the following statements: #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no1.0 1.0 #include ffnonbonded.itp

[gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?

Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am trying to get understanding the source codes. My basic understanding is that Gromacs has other approach of calculating dipole moment instead of the

Re: [gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?

On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote: Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am trying to get understanding the source codes. My basic understanding is that Gromacs has

Re: [gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/22/2010 04:35 PM, Carsten Kutzner wrote: On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote: Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am

Re: [gmx-users] CHARMM36 lipid bilayers

Hi there, Tom, many thanks for your valuable suggestions. I am also surprised by this large influence. For DPPC the change is about 5 A^2 (same settings but different water model). Cheers, Sven Pär Bjelkmar schrieb: I'm a bit surprised that the CHARMM tip3p makes a significant difference, how

[gmx-users] LJ cut-off distance

Dear all I have a system of polymer chains between 2 substrates. The substrates are FCC lattices consisting of Lennard-Jones particles.   I would like to know if it’s possible to handle individually the cut-off distances of the LJ interactions in the system For example, I would to use one

Re: [gmx-users] LJ cut-off distance

C. Batistakis wrote: Dear all I have a system of polymer chains between 2 substrates. The substrates are FCC lattices consisting of Lennard-Jones particles. I would like to know if it’s possible to handle individually the cut-off distances of the LJ interactions in the system For

Re: [gmx-users] LJ cut-off distance

Dear Justin Actually, what I want to do is to kill the attraction part of the LJ substrate-polymer interaction. So, I was thinking to put the cut-off equal the 1,12σ (point with the lowest energy). Do you have any other idea how can I have only the repulsion part? If not, can you suggest me

Re: [gmx-users] rlist and rcoulomb

Hello, Thanks for the reply. So, can I think that when I set rcoulomb rlist then the Coulomb (LR) energy term is providing some kind of correction over the Coulomb (SR) energy term. -Swarnendu On Thu, Oct 21, 2010 at 4:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: Swarnendu Tripathi

Re: [gmx-users] LJ cut-off distance

On 23/10/2010 2:08 AM, C. Batistakis wrote: Dear Justin Actually, what I want to do is to kill the attraction part of the LJ substrate-polymer interaction. So, I was thinking to put the cut-off equal the 1,12σ (point with the lowest energy). Mentioning the real objective, as well asking

Re: [gmx-users] rlist and rcoulomb

On 23/10/2010 2:20 AM, Swarnendu Tripathi wrote: Hello, Thanks for the reply. So, can I think that when I set rcoulomb rlist then the Coulomb (LR) energy term is providing some kind of correction over the Coulomb (SR) energy term. Yes. It's implementing the idea mentioned in the first

Re: [gmx-users] GPU slower than I7

Hi Roland, In fact I get better performance values using different rcoulomb, fourierspacing and the values of -npme suggested by g_tune_pme using -nt=12. The simulation using GPU was carried out using the dedicated machine, no other programs was runnig, even the graphical interface was stopped.

Re: [gmx-users] GPU slower than I7

Hi Szilárd, Thans for your explanation. Do you know if there will be a new improvement of PME algorithms to take the full advantage of GPU video cards? Do you think that the NODE and Real time difference could be attributed to some compilation problem in the mdrun-gpu. Despite I'm asking this I

Re: [gmx-users] LJ cut-off distance

Dear Mark Of course I agree with you but some times general knowledge is better than just solving a specific problem :-) In any case, many thanks for your answer and your time Best Regards, Chrysostomos --- Στις Παρ., 22/10/10, ο/η Mark Abraham mark.abra...@anu.edu.au έγραψε: Από: Mark

Re: [gmx-users] GPU slower than I7

Hi, On Fri, Oct 22, 2010 at 3:20 PM, Renato Freitas renato...@gmail.com wrote: Do you think that the NODE and Real time difference could be attributed to some compilation problem in the mdrun-gpu. Despite I'm asking this I didn't get any error in the compilation. It is very odd that these

[gmx-users] Error of particles communicated to PME node solved in Version4.5.1 ?

Hi, My system was well equilibrated, but still crashed within 1ns simulation due to the following information: Fatal error: 28 particles communicated to PME node 48 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. I wonder is this

Re: [gmx-users] Error of particles communicated to PME node solved in Version4.5.1 ?

Xu Danial wrote: Hi, My system was well equilibrated, but still crashed within 1ns simulation due to the following information: Fatal error: 28 particles communicated to PME node 48 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in

Re: [gmx-users] Error of particles communicated to PME node solved in Version4.5.1 ?

If you use v-rescale their is a very small probability that this is caused by a fixed error in GROMACS. On Fri, Oct 22, 2010 at 6:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: Xu Danial wrote: Hi, My system was well equilibrated, but still crashed within 1ns simulation due to the