Re: [gmx-users] the problem of the periodic boundary

kecy...@sina.com wrote: Hello, I use the 2D periodic boundary along the x and y axises, it has a strange thing. my solvent is dodecane, I view the output trajectory in the VMD, for one molecule, it has some part in the left(top), and some in the right(bottom), it still connections to each

[gmx-users] the problem of the periodic boundary

Hello, I use the 2D periodic boundary along the x and y axises, it has a strange thing. my solvent is dodecane,  I view the output  trajectory in the VMD, for one molecule, it has some part in the left(top), and some in the right(bottom), it still connections to each other, how to solve this pr

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Thanks Andreas. Is there any difference force-wise between this and our little workaround? Alex On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas wrote: > Hi, > > The POPC_53a6 topology works only with Gromacs versions lower than 4. > Please find attached the topology compatible with Gromacs4. >

RE: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Hi, The POPC_53a6 topology works only with Gromacs versions lower than 4. Please find attached the topology compatible with Gromacs4. I shall update files on the Gromacs website. Sorry for causing confusion. Best wishes Andreas From: gmx-users-boun...@g

Re: [gmx-users] trjconv => -[no]vel => print out the velocity ?

Chih-Ying Lin wrote: Hi Trjconv => with option "- [no] vel " what does the bracket "no" mean ? It indicates a boolean: -novel means do not write velocities, -vel means write velocities. Therefore, the presence or absence of a prefixed "no" determines the value. with the followin

[gmx-users] trjconv => -[no]vel => print out the velocity ?

Hi Trjconv => with option "- [no] vel " what does the bracket "no" mean ? with the following command, trjconv -f MD.trr -s MD.tpr -vel -o MD-test.gro the velocity is not print out on MD-test.gro. How to print out both the velocity and trajectory at the same time from .trr file? THank y

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks. Just in case anyone else is faced with the same issue, as far as forces are concerned, these dihedrals can be commented out. When considering the energy associated with dihedrals, just shift it appropriately. On Mon, May 3,

Re: [gmx-users] electrostatic interactions

On May 3, 2010, at 7:01 PM, abdullah ahmed wrote: I wish I could use a picture :) Unfortunately, this is not possible since I need the energy value to be able to compare this to other mutations of the same structure and to provide a "measure" of how energetically favourable one is in comp

RE: [gmx-users] electrostatic interactions

I wish I could use a picture :) Unfortunately, this is not possible since I need the energy value to be able to compare this to other mutations of the same structure and to provide a "measure" of how energetically favourable one is in comparison to the other. And I am using a box of water becau

Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

HAve look at the paper describing the topology ... On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote: Hello everyone, I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_to

[gmx-users] POPC 53a6 topology (dihedral multiplicity)

Hello everyone, I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies) for a simple lipid in water sim (gromacs version 4.0.5). I am using the lipid coordinates from the sa

Re: [gmx-users] electrostatic interactions

On May 3, 2010, at 6:40 PM, abdullah ahmed wrote: Actually I'd just like to know why both structures have such similar coloumb energy values. If an electro-static interaction is being made in one structure and not in the other then their coloumb energy values should be different too, no? W

RE: [gmx-users] electrostatic interactions

Actually I'd just like to know why both structures have such similar coloumb energy values. If an electro-static interaction is being made in one structure and not in the other then their coloumb energy values should be different too, no? Wouldn't this be visible with simple energy minimisatio

Re: [gmx-users] Unneccessary bonding

On May 3, 2010, at 6:27 PM, abdullah ahmed wrote: They are on the inside of the structure. I don't think it is caused by a water molecule, because I ran editconf and genbox again and got the same result. (I have assumed that water molecules are added to the structure in a random fashion in

[gmx-users] energy minimization + freeze atoms

Hello, I am trying to do energy minimization with normal mode analysis for my ststem. I used freezegrps and freezedim optitions to freeze the atoms. I found that after minimization the atoms are moved. Can you tell me how to freeze atoms for energy minimzation. I need this geometry for normal

RE: [gmx-users] electrostatic interactions

Thank you for your reply, Settings: I am using the procedure outline by the "speptide" tutorial (i.e. pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp" file I've used is as follows: ; User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp

Re: [gmx-users] Unneccessary bonding

abdullah ahmed wrote: They are on the inside of the structure. I don't think it is caused by a water molecule, because I ran editconf and genbox again and got the same result. (I have assumed that water molecules are added to the structure in a random fashion in areas not already occupied by

Re: [gmx-users] electrostatic interactions

abdullah ahmed wrote: Thank you for your reply, Settings: I am using the procedure outline by the "speptide" tutorial (i.e. pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp" file I've used is as follows: ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input fil

RE: [gmx-users] Unneccessary bonding

They are on the inside of the structure. I don't think it is caused by a water molecule, because I ran editconf and genbox again and got the same result. (I have assumed that water molecules are added to the structure in a random fashion in areas not already occupied by other atoms) If you lik

Re: [gmx-users] Unneccessary bonding

On May 3, 2010, at 6:12 PM, Justin A. Lemkul wrote: abdullah ahmed wrote: Dear Mr. Periole, The atoms that are getting close are oxygen from a GLU residue and hydrogen from a LYS residue. I don't see anything wrong with a 1.4-A distance between these atoms. Why do you suspect a proble

Re: [gmx-users] Unneccessary bonding

abdullah ahmed wrote: Dear Mr. Periole, The atoms that are getting close are oxygen from a GLU residue and hydrogen from a LYS residue. I don't see anything wrong with a 1.4-A distance between these atoms. Why do you suspect a problem (besides the non-existent bond)? -Justin Abdullah

Re: [gmx-users] electrostatic interactions

abdullah ahmed wrote: Hello everyone, I have just started using GROMACS, and apolise if my question is naive. Basically, I'd like to ask if anyone has some suggestions regarding the settings I should use for electrostatic interactions? Well, you haven't shown us what settings you're usin

RE: [gmx-users] Unneccessary bonding

Dear Mr. Periole, The atoms that are getting close are oxygen from a GLU residue and hydrogen from a LYS residue. Abdullah From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Unneccessary bonding Date: Mon, 3 May 2010 18:00:43 +0200 On May 3, 2010, at 5:52 PM, abdullah

[gmx-users] electrostatic interactions

Hello everyone, I have just started using GROMACS, and apolise if my question is naive. Basically, I'd like to ask if anyone has some suggestions regarding the settings I should use for electrostatic interactions? I have two protein molecules similar in everyway except, one has a single ne

Re: [gmx-users] Unneccessary bonding

On May 3, 2010, at 5:52 PM, abdullah ahmed wrote: Thank you very much for your reply, I agree it is probably a visualization of the effect, and that there is no bond. However, the distance between the two atoms participating in this "phantom bond" is 1.4 A°. Isn't that too close? Shouldn'

RE: [gmx-users] Unneccessary bonding

Thank you very much for your reply, I agree it is probably a visualization of the effect, and that there is no bond. However, the distance between the two atoms participating in this "phantom bond" is 1.4 A°. Isn't that too close? Shouldn't it be considered a clash? Abdullah From: x.peri.

Re: [gmx-users] Unneccessary bonding

On May 3, 2010, at 5:16 PM, abdullah ahmed wrote: Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is to run a few steps of minimization on a PDB structure and then obtain the energy value. To do so I ran the procedure suggested in the tutorial cal

[gmx-users] Unneccessary bonding

Hello, I am a new user to GROMACS and so this question maybe somewhat naive. My objective is to run a few steps of minimization on a PDB structure and then obtain the energy value. To do so I ran the procedure suggested in the tutorial called "speptide" using the .mdp file provided in this

[gmx-users] energy minimization + freeze atoms

Hello, I am trying to do energy minimization with normal mode analysis for my ststem. I used freezegrps and freezedim optitions to freeze the atoms. I found that after minimization the atoms are moved. Can you tell me how to freeze atoms for energy minimzation. I need this geometry for normal

RE: [gmx-users] cgnr in top file

Hi, This is not a decision, but a limitation of the grompp code. I have fixed this in the git release. Simply editing the charge group numbers by hand to make them all different should work. Berk > Date: Mon, 3 May 2010 10:22:54 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subje

Re: [gmx-users] cgnr in top file

Erik Marklund wrote: True. I guess gromacs groups together the terminal hydrogens, overriding the original force field parameters. Can't say why that decision was made, but it will influence your simulation very little. I think there was a bug report some time ago involving virtual sites on

Re: [gmx-users] cgnr in top file

True. I guess gromacs groups together the terminal hydrogens, overriding the original force field parameters. Can't say why that decision was made, but it will influence your simulation very little. Erik leila karami skrev: Dear Erik you said Amber03 was not parameterized with charge groups

[gmx-users] cgnr in top file

Dear Erik you said Amber03 was not parameterized with charge groups and last column in your rtp entry holds the chargegroup numbers. but cgnr column in my top file does not looks just like it. in case of H1, H2 and H3. * H1amber99_17 0.16420 2 ** H2amber99_17 0.16420 3

Re: [gmx-users] cgnr in top file

leila karami wrote: Dear Erik thank for your answer. my rtp file for amber 03 force field is as follow : [ NGLY ] [ atoms ] Namber99_39 0.29430 1 H1amber99_17 0.16420 2 H2amber99_17 0.16420

Re: [gmx-users] cgnr in top file

The last column in your rtp entry holds the chargegroup numbers. The cgnr column in your top file looks just like it. Amber03 was not parameterized with charge groups, so the atoms are not groupt together as you can see. Erik leila karami skrev: Dear Erik thank for your answer. my rtp fi

[gmx-users] cgnr in top file

Dear Erik thank for your answer. my rtp file for amber 03 force field is as follow : [ NGLY ] [ atoms ] Namber99_39 0.29430 1 H1amber99_17 0.16420 2 H2amber99_17 0.16420 3 H3amber99_17 0.16420 4 CAamber99_11 -0.01000 5 HA1

Re: [gmx-users] cgnr in top file

Erik Marklund skrev: leila karami skrev: Hi all how cgnr is determind in *.top file? based on? Any help will highly appreciated! Depends on the force field. Generally, they're set according to the chargegroups in the original force field, if the force field was parameterized with charge

Re: [gmx-users] cgnr in top file

leila karami skrev: Hi all how cgnr is determind in *.top file? based on? Any help will highly appreciated! Depends on the force field. Generally, they're set according to the chargegroups in the original force field, if the force field was parameterized with charge groups, that is. --

[gmx-users] cgnr in top file

Hi all how cgnr is determind in *.top file? based on? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscrib

Re: [gmx-users] Help for running gromacs

I will download latest version of gromacs and start working with it.I will be back if any face any problem. Thanks to all On Mon, May 3, 2010 at 6:39 PM, Justin A. Lemkul wrote: > > What compilers did you use to install Gromacs? Often times hangs and other > memory errors are related to buggy c

Re: [gmx-users] Help for running gromacs

What compilers did you use to install Gromacs? Often times hangs and other memory errors are related to buggy compilers. -Justin priyanka panwar wrote: Command line was " genion -s em.tpr -o ions.pdb -np 4" On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul > wrote:

Re: [gmx-users] Help for running gromacs

-np is not about number of processors in the case of genion. It's the number of positive ions to insert. shaya...@post.tau.ac.il skrev: Hi, No need to include "-np 4" at all. genion command does not take advantage of multiple processors (nor does it need to). Try rerunning the command withou

Re: [gmx-users] Help for running gromacs

Hi, I tried it that way also, but in that case it displays a message "No ions to add and no potential to generate" and it is also not generating ions.pdb file but it is creating genion.log file. On Mon, May 3, 2010 at 6:02 PM, wrote: > Hi, > No need to include "-np 4" at all. genion command does

Re: [gmx-users] Help for running gromacs

Hi, No need to include "-np 4" at all. genion command does not take advantage of multiple processors (nor does it need to). Try rerunning the command without -np 4. -Shay Quoting "priyanka panwar" : Command line was " genion -s em.tpr -o ions.pdb -np 4" On Mon, May 3, 2010 at 5:19 PM, Jus

Re: [gmx-users] Help for running gromacs

Command line was " genion -s em.tpr -o ions.pdb -np 4" On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul wrote: > > > priyanka panwar wrote: > >> Hi, >> Thanks for help. >> -Command line was: >> Number of (3-Atomic) solvent molecules:4256 >> Replacing solvent molecule 499 (atom 2784) with Na >> >

Re: [gmx-users] Help for running gromacs

priyanka panwar wrote: Hi, Thanks for help. -Command line was: Number of (3-Atomic) solvent molecules:4256 Replacing solvent molecule 499 (atom 2784) with Na That's not a command line. What command did you actually type (exactly) to run genion? -Group selected was: 12 (SOL) -Gromacs vers

Re: [gmx-users] Help for running gromacs

Hi, Thanks for help. -Command line was: Number of (3-Atomic) solvent molecules:4256 Replacing solvent molecule 499 (atom 2784) with Na -Group selected was: 12 (SOL) -Gromacs version I am using is 3.3.1 On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk wrote: > Please post more details includin

Re: [gmx-users] Help for running gromacs

Please post more details including the following: - What is the exact command line? - What group do you select as a "continuous solvent"? I know it might sound weird to ask this but what I learned while teaching students is that these questions really should be asked when there are pro

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Thank you Jochem, In your last reply, did you mean that i can perform the WHAM on Various histograms that were collected with different force constants? i mean , will it know to do the correction for the biasing potential Yes, WHAM does not require identical force consta