Re: [gmx-users] scaling non-bonded interactions

On 1/06/2011 6:59 PM, Kukol, Andreas wrote: Hello, Is it possible to globally scale all non-bonded interactions by a factor ? I know there are energy exclusion groups, but that is an all or nothing approach, while I would like to reduce non-bonded interaction potentials to e.g. 10% of their

[gmx-users] viscosity

Hello, I calculate the viscosity with g_energy using option -vis (Gromacs 4.0.7): g_energy -f file.trr -s file.tpr -vis visc.xvg Why do I get viscosity values only until the half of the simulation time? Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Re: question about trajcat command: Merge files

Miguel Quiliano Meza wrote: Dear Justin. Thank you for you answer. But, the case I wrote, it was an ideally case. To help anyone in the forum at the same time. As soon as I have read your answer I tried. In my case my simulations were: First simulation: 0.4ns Second : 1ns Third: 2ns Fourt

[gmx-users] Re: question about trajcat command: Merge files

anlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.

Re: [gmx-users] scaling non-bonded interactions

Kukol, Andreas wrote: FudgeLJ does only work when the pairs are generated automatically. If they are specified explicitly as in the Gromos forcefields, FudgeLJ has no effect. I see two ways to get around this problem: 1. Specify pairs manually (which may be tedious) 2. Minimize with a forc

RE: [gmx-users] scaling non-bonded interactions

FudgeLJ does only work when the pairs are generated automatically. If they are specified explicitly as in the Gromos forcefields, FudgeLJ has no effect. Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lem

RE: [gmx-users] question about trajcat command: Merge files

Use trajcat with the option -settime then you can specify the starting time for each simulation interactively. Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Miguel Quiliano Meza [rifaxim...@gmail.com] Sent: 01 Ju

RE: [gmx-users] Re: scaling non-bonded interactions

I want to use it to energy minimise a system that has severe clashes. The EM always crashes, even if I reduce the step-size. It could also be useful for NMR refinement to allow atoms to move through each other in order to satisfy distance restraints. Andreas

Re: [gmx-users] question about trajcat command: Merge files

Miguel Quiliano Meza wrote: Dear community, I have a couple of doubts, please help me to clarify. I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns ,4ns) , they are only a continuation of the last, because of I was explored the rmsd variation along the time. Now I want t

Re: [gmx-users] scaling non-bonded interactions

Da-Wei Li wrote: I remember that 1-4 won't be scaled in the free energy code, right? True, but the desired 10% scaling in this case can be applied by changing the FudgeLJ and FudgeQQ values of the force field, I believe. -Justin dawei On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul

Re: [gmx-users] Re: scaling non-bonded interactions

Vitaly Chaban wrote: Doesn't increased temperature work for this purpose? REMD can be useful, yes, but generalized Hamiltonian exchange, using lambda to scale the interactions between molecules can be very effective, as well. -Justin On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul w

[gmx-users] question about trajcat command: Merge files

Dear community, I have a couple of doubts, please help me to clarify. I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns ,4ns) , they are only a continuation of the last, because of I was explored the rmsd variation along the time. Now I want to merge all the trajectories to do

Re: [gmx-users] scaling non-bonded interactions

I remember that 1-4 won't be scaled in the free energy code, right? dawei On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul wrote: > > > Kukol, Andreas wrote: > >> Hello, >> Is it possible to globally scale all non-bonded interactions by a factor ? >> I know there are energy exclusion groups, b

Re: [gmx-users] Re: scaling non-bonded interactions

Doesn't increased temperature work for this purpose? On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul wrote: > > > Vitaly Chaban wrote: >>> >>> Is it possible to globally scale all non-bonded interactions by a factor >>> ?  I know there are energy exclusion groups, but that is an all or nothing

Re: [gmx-users] Re: scaling non-bonded interactions

Vitaly Chaban wrote: Is it possible to globally scale all non-bonded interactions by a factor ? I know there are energy exclusion groups, but that is an all or nothing approach, while I would like to reduce non-bonded interaction potentials to e.g. 10% of their normal value. If this is not

Re: [gmx-users] scaling non-bonded interactions

Kukol, Andreas wrote: Hello, Is it possible to globally scale all non-bonded interactions by a factor ? I know there are energy exclusion groups, but that is an all or nothing approach, while I would like to reduce non-bonded interaction potentials to e.g. 10% of their normal value. If t

[gmx-users] Re: scaling non-bonded interactions

> > Is it possible to globally scale all non-bonded interactions by a factor ?  I > know there are energy exclusion groups, but that is an all or nothing > approach, while I would like to reduce non-bonded interaction potentials to > e.g. 10% of their normal value. > > If this is not possible, I

Re: [gmx-users] compression to study pressure effect

Elisabeth wrote: Dear all, I am trying to study the effect of pressure on total potential of my system (8 polymer chains). My problem is that I dont see a systematic effect of pressure on potentials and I cant judge if different pressures increase or decrease potential. This is the critical

[gmx-users] Re: compression to study pressure effect

Either a tighter pressure coupling time... On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban wrote: > Hmm... > > > 1. The background of the task is not quite clear for me. > > 2. Evidently, the fluctuations are higher than the difference for your > pressures. > > 3. Why not to use significantly la

[gmx-users] Re: compression to study pressure effect

Hmm... 1. The background of the task is not quite clear for me. 2. Evidently, the fluctuations are higher than the difference for your pressures. 3. Why not to use significantly larger systems and significantly larger difference between pressures? -- Dr. Vitaly V. Chaban, Department of Chem

Re: [gmx-users] implicit solvent LINCS errors

This isn't surprising. Pressure coupling without explicit solvent doesn't work the way that you are anticipating. You might want to look at what happened to the system using ngmx or VMD to see what went wrong. Unless you need to simulate in a box for some reason, you should turn off PBC as Justin

Re: [gmx-users] scaling non-bonded interactions

hello I do not know whether there is an option but you can achieve this easily by revising top file. dawei On Wed, Jun 1, 2011 at 4:59 AM, Kukol, Andreas wrote: > Hello, > > Is it possible to globally scale all non-bonded interactions by a factor ? > I know there are energy exclusion groups,

[gmx-users] scaling non-bonded interactions

Hello, Is it possible to globally scale all non-bonded interactions by a factor ? I know there are energy exclusion groups, but that is an all or nothing approach, while I would like to reduce non-bonded interaction potentials to e.g. 10% of their normal value. If this is not possible, I sug

[gmx-users] compression to study pressure effect

Dear all, I am trying to study the effect of pressure on total potential of my system (8 polymer chains). My problem is that I dont see a systematic effect of pressure on potentials and I cant judge if different pressures increase or decrease potential. This is the critical observable in my system

Re: [gmx-users] implicit solvent LINCS errors

Scratch what I said last night about pressure coupling - it crashes after ~200K timesteps due to fluctuations in the cell volume. I'm sticking with NVT for now. On 5/31/2011 6:14 PM, Michael Daily wrote: The following mdp file produces a successful dynamics run out to 100K steps / 200 ps. Wh

Re: [gmx-users] .gro to .pqr

Hi Mona, You can try to convert your .gro file in .pdb. Then you can use pdb2pqr.py, that permits to assign atomic charges basing on AMBER or CHARMM force-field Francesco Il 01/06/2011 17:22, Justin A. Lemkul ha scritto: Mona Habibi wrote: Hi Justin, Thank you for quick answer, but I

Re: [gmx-users] .gro to .pqr

Mona Habibi wrote: Hi Justin, Thank you for quick answer, but I don't have the .tpr file, Is there any other way? No. The only file format that contains all the information necessary for a .pqr file (coordinates, charges, and radii) is a .tpr file. Generating one is trivial; follo

Re: [gmx-users] .gro to .pqr

Hi Justin, Thank you for quick answer, but I don't have the .tpr file, Is there any other way? On Wed, Jun 1, 2011 at 11:13 AM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> Mona Habibi wrote: >> >>> Hi, >>> I have a single file in .gro format and I want to change it to

Re: [gmx-users] .gro to .pqr

Justin A. Lemkul wrote: Mona Habibi wrote: Hi, I have a single file in .gro format and I want to change it to pqr format. I was wondering if there is anyway to make it? I tried to write the file with exactly the same format of pqr , but VMD can not read my file. editconf -mead outputs

Re: [gmx-users] .gro to .pqr

Mona Habibi wrote: Hi, I have a single file in .gro format and I want to change it to pqr format. I was wondering if there is anyway to make it? I tried to write the file with exactly the same format of pqr , but VMD can not read my file. editconf -mead outputs a .pqr file from an input coo

[gmx-users] .gro to .pqr

Hi, I have a single file in .gro format and I want to change it to pqr format. I was wondering if there is anyway to make it? I tried to write the file with exactly the same format of pqr , but VMD can not read my file. Thank You. -- Mona Habibi Ph.D student Biological and Condensed Matter Physi

Re: [gmx-users] Steered Molecular dynamics

bharat gupta wrote: Hi, I want to know is there any well documented tutorial for SMD in gromacs ?? Have you checked the "Tutorials" page on the Gromacs site? http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling If you're wondering about tutorials, that's the plac

[gmx-users] Steered Molecular dynamics

Hi, I want to know is there any well documented tutorial for SMD in gromacs ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51

Re: [gmx-users] flexibility

Hi Tsjerk, thanks for nice the reference. If I have understood correctly, the authors have applied their technique to characterize the residues and the respective motions that confer thermal stability to a thermophilic enzyme compared to a mesophilic homologue. In my case I want to study the effec

Re: [gmx-users] g_covar

Thanks Sir, Thanks just now I figured it out! With regards kavya On Wed, Jun 1, 2011 at 6:20 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > Each atom has three coordinates; 3*3740=11220 coordinates, yielding as > many eigenvalues and -vectors. > > Cheers, > > Tsjerk > > On Wed, Jun 1, 2011 at 2:4

Re: [gmx-users] g_covar

Hi Kavya, Each atom has three coordinates; 3*3740=11220 coordinates, yielding as many eigenvalues and -vectors. Cheers, Tsjerk On Wed, Jun 1, 2011 at 2:44 PM, Kavyashree M wrote: > Dear users, > > I was using g_covar (gmx 4.5.3) to find the eigenvalue and > eigenvectors. When I used f

[gmx-users] g_covar

Dear users, I was using g_covar (gmx 4.5.3) to find the eigenvalue and eigenvectors. When I used for "protein" which is actually - 3740 in number, it gave a total of 11220 eigenvalues, similarly for bacbone, c-alpha atoms, the number of eigenvalues given was not matching with the number o

Re: [gmx-users] flexibility

Hi, The usual (statistical) way to compare fluctuations (variances) is by taking the ratio (i.e. of the MSFs, not the RMSFs). Maragliano e.a. (BiophysJ 2004) wrote on such comparison of fluctuations, using a variance ratio test. In your case, you'd have to combine it with a structure alignment to

Re:Re: AW: Re: [gmx-users] where can I download POPC membrane file?

Maybe you think it is a simple scrips, but for those fresh GROMACS user such as me, it would be a very difficult task. Anyway, thanks a lot for the messages. At 2011-06-01，"Thomas Piggot" wrote: >In addition to all the other responses, I just wanted to clear up why >there is this difference

Re: [gmx-users] flexibility

shiva birgani wrote: Message: 1 Date: Tue, 31 May 2011 06:56:16 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] flexiblity To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Message-ID: <4de4c950.70...@vt.edu

Re: AW: Re: [gmx-users] where can I download POPC membrane file?

In addition to all the other responses, I just wanted to clear up why there is this difference in names. The POPC structure from the link below still has the atom names of the old CHARMM27 lipids (DPPC is fine). As suggested, a simple script can do the conversion for you. Cheers Tom albert wrote

Re: [gmx-users] Gravity force in equation of motion

Thank you for your reply. I think so On Wed, Jun 1, 2011 at 12:01 PM, Jianguo Li wrote: > Seems gravity is much weaker than the other forces in molecular simulations > and thus can be neglected. > Jianguo > > -- > *From:* mohsen ramezanpour > *To:* Discussion list f

Re: [gmx-users] Gravity force in equation of motion

Seems gravity is much weaker than the other forces in molecular simulations and thus can be neglected. Jianguo From: mohsen ramezanpour To: Discussion list for GROMACS users Sent: Wednesday, 1 June 2011 15:20:09 Subject: [gmx-users] Gravity force in equation

[gmx-users] Gravity force in equation of motion

Dear All There is a question about applied forces in MD equations of motion. Where do we insert Gravity in our equation? In the other words : Had we ignored gravity force in our equations? Why? Actually I read manual but I weren't answered. Thanks in advance -- gmx-users mailing listgmx-use

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 209

> Message: 1 > Date: Tue, 31 May 2011 06:56:16 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] flexiblity > To: Discussion list for GROMACS users > Message-ID: <4de4c950.70...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > shiva birgani wrote: > > Dear a