[gmx-users] Re: Advantage of NPT over NVT?

If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

Re: [gmx-users] forcefield

Hi Lalitha, Zebularine is beyond the trivial. You may be able to derive something reasonable from the other bases using 'chemical intuition' (cytidine, thymidine, uracil), but it's likely that the electronic structure of the ring is too different to justify an approach like that. Likely you should

Re: [gmx-users] run g_cover in parallel

Hi, >> I wonder if there a way to run g_cover in paralel in order to make >> things run faster? > > No. Obviously you can use -dt to reduce the number of frames you analyze. In most cases it's not the reading of frames, but the diagonalization of the covariance matrix that consumes most of the ti

Re: [gmx-users] Re: Advantage of NPT over NVT?

Vitaly V. Chaban wrote: If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Sounds dangerous :-) If the model produces a wrong density, you'd want to be reasonably confident your observable is not l

Re: [gmx-users] run g_cover in parallel

Tsjerk Wassenaar wrote: Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? No. Obviously you can use -dt to reduce the number of frames you analyze. In most cases it's not the reading of frames, but the diagonalization of the covariance matrix that cons

Re: [gmx-users] What is best way to get multiple chains?

Mark Abraham ha scritto: > ms wrote: >> Hi, >> >> I am a gmx newbie, so please don't bite too much! :) >> >> Learning gmx, I am experimenting with simulations with multiple >> identical small chains. What I did was: >> >> - I generated the peptides with pymol >> - Generated a .gro with pdb2gmx > >

Re: [gmx-users] What is best way to get multiple chains?

ms wrote: Mark Abraham ha scritto: ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx This step is

Re: [gmx-users] What is best way to get multiple chains?

ms wrote: Mark Abraham ha scritto: ms wrote: Hi, I am a gmx newbie, so please don't bite too much! :) Learning gmx, I am experimenting with simulations with multiple identical small chains. What I did was: - I generated the peptides with pymol - Generated a .gro with pdb2gmx This step is "g

[gmx-users] unit of eigenfrequency

Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me.

Re: [gmx-users] What is best way to get multiple chains?

Mark Abraham ha scritto: > ms wrote: >> Mark Abraham ha scritto: >>> What do you want the chain identifiers for? I'm not aware of a >>> post-pdb2gmx purpose that they might serve. >> >> This is where my naivety probably enters in: Analysis programs work on >> groups. If several chains are defined,

Re: [gmx-users] What is best way to get multiple chains?

ms wrote: Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do you mind if I later I try to update the "multiple chains" wiki page based on your advices? Updates from users who have relevant experience is what continually makes the documentation better! The section on "

[gmx-users] Re: Advantage of NPT over NVT?

> Vitaly V. Chaban wrote: >> If your model gives a correct fluid density with NPT, use NPT. If it >> does not, then use NVT. >> This is a quick practical guide, not not read much. :) > > Sounds dangerous :-) If the model produces a wrong density, you'd want > to be reasonably confident your observa

Re: [gmx-users] Re: Advantage of NPT over NVT?

Vitaly V. Chaban wrote: Vitaly V. Chaban wrote: If your model gives a correct fluid density with NPT, use NPT. If it does not, then use NVT. This is a quick practical guide, not not read much. :) Sounds dangerous :-) If the model produces a wrong density, you'd want to be reasonably confident y

Re: [gmx-users] grompp: no such moleculetype

Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as with my protein. I started fro

Re: [gmx-users] grompp: no such moleculetype

Francesco Pietra wrote: Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiquitin which is provided on the MARTINI web page. I encountered the same problem as wit

Re: [gmx-users] grompp: no such moleculetype

On Wed, Oct 14, 2009 at 7:22 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hi Justin: >> Back from the Austrian mountains, to further isolate problems I >> encountered before with my protein, I have tried to reproduce - at the >> lowest stage - the CG tutorial for ubiquitin which

Re: [gmx-users] grompp: no such moleculetype

Francesco Pietra wrote: On Wed, Oct 14, 2009 at 7:22 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: Hi Justin: Back from the Austrian mountains, to further isolate problems I encountered before with my protein, I have tried to reproduce - at the lowest stage - the CG tutorial for ubiqu

[gmx-users] question about all atoms lipid molecule structure and force field

Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar wit

Re: Re: [gmx-users] RMSF reference state?

Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this?"With the option -od the root mean square deviation with respect to the reference structure is calculated" What about without -od, should there be no reference structure or

[gmx-users] weird tabulated potential problem

Hi, Some months ago I reported a strange conflict between the GMX 4 new option nblist=-1 and tabulated potentials. At that time I contacted Berk and he could run my test system without any problem. So I thought I had something wrong for my system configurations. However, recently I re-checked t

RE: [gmx-users] question about all atoms lipid molecule structure and force field

Hi, You can find some configurations here: http://persweb.wabash.edu/facstaff/fellers/ And I think you can use Charmm FF. Lanyuan Date: Wed, 14 Oct 2009 11:29:26 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about all atoms lipid molecule structure and

Re: Re: [gmx-users] RMSF reference state?

Hi Pan Wu, There are two things to distinguish: 1. The reference structure used to remove translational and rotational degrees of freedom 2. The reference against which the deviations (on a per atom base) are calculated that are then squared, averaged and taken the root of (root mean square fluct

Re: [gmx-users] RMSF reference state?

Pan Wu wrote: Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? "With the option -od the root mean square deviation with respect to the reference structure is calculated" What about without -od, should there be no ref

Re: [gmx-users] RMSF reference state?

Hi, Actually, Justin is completely right (and I should've checked g_rmsf -h). -od calculates the RMSD from the structure in the frame against the structure in the topology file. This does not nullify the statements regarding references for fitting and references for deviations though :p Cheers,

[gmx-users] simulation end with Segmentation fault, error message said something about libSystem.B.dylib

Hi, Lately few of my simulations had ended up with wired output: Writing final coordinates. step 50, remaining runtime: 0 s [xn068:94365] *** Process received signal *** [xn068:94365] Signal: Segmentation fault (11) [xn068:94365] Signal code: Address not mapped (1) [xn068:94365] Failing a

Re: [gmx-users] simulation end with Segmentation fault, error message said something about libSystem.B.dylib

Itamar Kass wrote: Hi, Lately few of my simulations had ended up with wired output: Writing final coordinates. step 50, remaining runtime: 0 s [xn068:94365] *** Process received signal *** [xn068:94365] Signal: Segmentation fault (11) [xn068:94365] Signal code: Address not map

Re: [gmx-users] question about all atoms lipid molecule structure and force field

Thank you, Is it really necessary for me to use Charmm FF for all atom calculations on lipids? The reason I am asking this is because it will require me to create gromacs compatible FF files of the Charmm FF . I did find two perl scripts which can do probably handle that but i am wondering if the

Re: [gmx-users] question about all atoms lipid molecule structure and force field

Amit Choubey wrote: Thank you, Is it really necessary for me to use Charmm FF for all atom calculations on lipids? You can use whatever model you want, provided it's valid. Just so happens that most people who use all-atom models of lipids use CHARMM. The reason I am asking this is be

[gmx-users] Fwd: unit of eigenfrequency

Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me.

Re: [gmx-users] simulation end with Segmentation fault, error message said something about libSystem.B.dylib

On Thu, Oct 15, 2009 at 1:40 PM, Mark Abraham wrote: > Itamar Kass wrote: > >> Hi, >> >> Lately few of my simulations had ended up with wired output: >> >> Writing final coordinates. >> step 50, remaining runtime: 0 s [xn068:94365] *** Process >> received signal *** >> [xn068:94365