Re: [gmx-users] Box size increases in NPT

On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely

Re: [gmx-users] Box size increases in NPT

If the job is not very parallel, it will not crash. It is better to preequilibrate in NVT beforehand. Cyclopropylchloride is probably a liquid at 290K, if the model is parametrized reasonably. So it should not phase-separate. Vitaly On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham

Re: [gmx-users] Box size increases in NPT

By crash I meant explode not DD is impossible. Explosions don't happen because of parallelism, they happen because the steps are too large for the size of the forces. The forces required to stably expand a box from 20A to 70A seem likely to be so large that I am very skeptical that you could

[gmx-users] Box size increases in NPT

Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and

[gmx-users] Box size/type confusion for bilayer system

Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not standard cubes. I'm trying to run a membrane simulation where a cyclic undecapeptide is inserted into the membrane and I want the water layer to be sufficiently thick that if it were pulled, the

Re: [gmx-users] Box size/type confusion for bilayer system

On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not standard cubes. I'm trying to run a membrane simulation where a cyclic undecapeptide is inserted into the membrane and I want the water layer to be sufficiently

Re: [gmx-users] Box size/type confusion for bilayer system

On 10/18/2012 11:53 AM, Justin Lemkul wrote: On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not standard cubes. I'm trying to run a membrane simulation where a cyclic undecapeptide is inserted into the membrane

Re: [gmx-users] Box size/type confusion for bilayer system

On 10/18/12 3:04 PM, klexa wrote: On 10/18/2012 11:53 AM, Justin Lemkul wrote: On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not standard cubes. I'm trying to run a membrane simulation where a cyclic

Re: [gmx-users] Box size/type confusion for bilayer system

On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote: On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not standard cubes. I'm trying to run a membrane simulation where a cyclic undecapeptide is inserted

Re: [gmx-users] Box size/type confusion for bilayer system

On 10/18/12 3:55 PM, Peter C. Lai wrote: On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote: On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not standard cubes. I'm trying to run a membrane simulation where a

Re: [gmx-users] Box size/type confusion for bilayer system

On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote: On 10/18/12 3:55 PM, Peter C. Lai wrote: On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote: On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about the proper way to handle boxes that are not

[gmx-users] Box size/type confusion for bilayer system

Previous message: [gmx-users] Box size/type confusion for bilayer system Next message: [gmx-users] Box size/type confusion for bilayer system Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] On 10/18/12 2:43 PM, klexa wrote: Hi Gromacs users, I think I am a bit confused about

Re: [gmx-users] Box Size in MD

lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org Gesendet: 17:28 Donnerstag, 22.März 2012 Betreff: Re: [gmx-users] Box Size in MD Lara Bunte wrote: Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions

Re: [gmx-users] Box Size in MD

Lara *Von:* Justin A. Lemkul jalem...@vt.edu *An:* Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org *Gesendet:* 17:28 Donnerstag, 22.März 2012 *Betreff:* Re: [gmx-users] Box Size in MD

[gmx-users] Box Size in MD

Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Box Size in MD

As far as I concern, the minimum size is that cove all parts of your molecules or system. In case you should use solvent it is up to you to add how many molecules and in this case you should make decision by experience or according to literature. Dariush -- Kind Regards, Dariush Mohammadyani

Re: [gmx-users] Box Size in MD

Hi Lara, The cut-offs are pretty much part of the force field. One rule is that the distance between periodic images should be larger than the cutoff. For protein/solute simulations that translates in a minimal distance between the solute and the wall of half the cutoff used. Another rule is

Re: [gmx-users] Box Size in MD

Lara Bunte wrote: Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? This is not correct. The cutoffs are dictated by the force field

[gmx-users] Box-size: please reply

Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift

Re: [gmx-users] Box-size: please reply

This mail was answered already... Please pay attention. http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html Tsjerk On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating the box dimensions during a simulation of 20ns I got some

Re: [gmx-users] Box-size: please reply

Sorry Sir, I did not get that mail from the forum. Thank you With Regards Kavya On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: This mail was answered already... Please pay attention. http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html Tsjerk

Re: [gmx-users] Box-size: please reply

Sir, I checked gmxdump -e ener.edr as suggested, I found that there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5 when I calculated the average for these values using another tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave some different answer as mentioned before in both

Re: [gmx-users] Box-size: please reply

On 17/08/2011 9:13 PM, Kavyashree M wrote: Sir, I checked gmxdump -e ener.edr as suggested, I found that there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5 when I calculated the average for these values using another tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave some

[gmx-users] Box-size

Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est. RMSD Tot-Drift

Re: [gmx-users] Box-size

On 16/08/11, Kavyashree M hmkv...@gmail.com wrote: Dear users, While calculating the box dimensions during a simulation of 20ns I got some strange values of the averages - Command used: g_energy -f ener.edr -o box.xvg Output: Energy Average Err.Est.

[gmx-users] Box size error during attempted NPT equilibration

Hi, I have tried to run a simulation of 1000 SPC/E water molecules. I have a PDB file containing a 10 by 10 by 10 regular array (cube) of water molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to convert the PDB file to GRO and topology, selecting the OPLS-AA force field

Re: [gmx-users] Box size error during attempted NPT equilibration

Andrew DeYoung wrote: Hi, I have tried to run a simulation of 1000 SPC/E water molecules. I have a PDB file containing a 10 by 10 by 10 regular array (cube) of water molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to convert the PDB file to GRO and topology, selecting

Re: [gmx-users] Box size and potential energy calculation

Am Sonntag, den 23.01.2011, 09:40 +1100 schrieb Mark Abraham: On 23/01/2011 2:36 AM, Christian Mötzing wrote: Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham: On 21/01/2011 6:47 AM, Christian Mötzing wrote: Hi, I currently read through the GMX manual 4.5.3. I have two

Re: [gmx-users] Box size and potential energy calculation

On 1/23/11 12:58 PM, Christian Mötzing wrote: Am Sonntag, den 23.01.2011, 09:40 +1100 schrieb Mark Abraham: On 23/01/2011 2:36 AM, Christian Mötzing wrote: Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham: On 21/01/2011 6:47 AM, Christian Mötzing wrote: Hi, I currently read

Re: [gmx-users] Box size and potential energy calculation

Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham: On 21/01/2011 6:47 AM, Christian Mötzing wrote: Hi, I currently read through the GMX manual 4.5.3. I have two questions: 1) Density is calculated by the density of the material and the box volume. But I can't find a

Re: [gmx-users] Box size and potential energy calculation

On 23/01/2011 2:36 AM, Christian Mötzing wrote: Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham: On 21/01/2011 6:47 AM, Christian Mötzing wrote: Hi, I currently read through the GMX manual 4.5.3. I have two questions: 1) Density is calculated by the density of the material and

Re: [gmx-users] Box size and potential energy calculation

On 21/01/2011 6:47 AM, Christian Mötzing wrote: Hi, I currently read through the GMX manual 4.5.3. I have two questions: 1) Density is calculated by the density of the material and the box volume. But I can't find a reference on how the box size is calculated. Can you point me to some

[gmx-users] Box size and potential energy calculation

Hi, I currently read through the GMX manual 4.5.3. I have two questions: 1) Density is calculated by the density of the material and the box volume. But I can't find a reference on how the box size is calculated. Can you point me to some literature? 2) I wanted to look up the calculation of the

[gmx-users] box size continuing the previous energy minimization

Hi, 1. How can I learn the box shape and size of a completed simulation? 2. I want to keep going the previous completed energy minimization by increasing nsteps. How can I do this? Best wishes Mustafa -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] box size continuing the previous energy minimization

On Fri, Dec 24, 2010 at 8:12 AM, Amit Choubey kgp.a...@gmail.com wrote: On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel mfbil...@gmail.comwrote: Hi, 1. How can I learn the box shape and size of a completed simulation? check the end of the resulting gro file . 2. I want to keep going

[gmx-users] box size

Dear all, I am new about MD simulation and I have some questions about the box size. I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm ) but now I change to a bigger molecules and increase the number of molecules. So,the new system cannot fix into the previous box.

Re: [gmx-users] box size

noob noob wrote: Dear all, I am new about MD simulation and I have some questions about the box size. I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm ) but now I change to a bigger molecules and increase the number of molecules. So,the new system cannot fix into

RE: [gmx-users] box size changing during isotropic pressure coupling

and y are treated differently (although adding only zeros), so depending on the compiler, the results could differ by a bit. What system and compiler are you using? Berk. Date: Fri, 18 Jul 2008 13:54:19 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] box size

Re: [gmx-users] box size changing during isotropic pressure coupling

doesn't seem to exist anymore. Berk. Date: Fri, 18 Jul 2008 13:54:19 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] box size changing during isotropic pressure coupling Hello, I have a system of 750,000 atoms consisting of detergent in water

RE: [gmx-users] box size changing during isotropic pressure coupling

math, so I can not see if somehow this would make numbers slightly below 20 scale down and above 20 scale up. Berk. Date: Thu, 24 Jul 2008 13:40:02 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] box size changing during isotropic pressure coupling Berk

[gmx-users] box size changing during isotropic pressure coupling

Thanks for the assistance Berk, Hmm... this is a (seemingly( really systematic decrease in x and y and increase in z. But is x at the start really EXACTLY identical to y? No. Here are the starting dimensions: 19.58000 19.39000 21.04200 That is prior to 200ps run with position

[gmx-users] box size changing during isotropic pressure coupling

Here tau_p=4, which is already quite large. But there are no real problems in the system, the results should be fine. But the relative ling tau_p might be the reason for the strange scaling. This would make the scaling factor always close to 1 plus or minus one bit. I have not done the binary

RE: [gmx-users] box size changing during isotropic pressure coupling

it has been fixed for 4.0. Berk. Date: Thu, 24 Jul 2008 14:55:24 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] box size changing during isotropic pressure coupling Here tau_p=4, which is already quite large. But there are no real problems in the system

[gmx-users] box size changing during isotropic pressure coupling

A knowledgeable and helpful gromacs user has pointed me to some bugzilla comments: http://bugzilla.gromacs.org/show_bug.cgi?id=165 that reference revision comments: http://www.gromacs.org/gromacs/revisions/ Berk Hess 13 Feb 2008 box distortion with pressure coupling In all Gromacs

[gmx-users] box size

Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? 2. for the editconf command, editconf -d Distance_between_the_solute_and_the_box bt cubic Right?? what are the differences between the three number in

Re: [gmx-users] box size

Chih-Ying Lin wrote: Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? These values represents the real dimensions of the box 2. for the editconf command, editconf -d

Re: [gmx-users] box size

Hi, Read a bit more carefully though. A cubic box is based on the circumscribed sphere of the solute, dilated with the desired distance between the solute and the wall (and it has nothing to do with calculation of the solvation surface, which to me sounds to be related to solvent accessible

[gmx-users] Box size Increase

Hello, I was trying to run a simple LJ system. In the conf.gro box size is 7.52 (cubic). But in the confout.gro the box size is 9.1. Is this possible? -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

Re: [gmx-users] Box size Increase

Arnab Senapati wrote: Hello, I was trying to run a simple LJ system. In the conf.gro box size is 7.52 (cubic). But in the confout.gro the box size is 9.1. Is this possible? Yes, since it happened. :-) If you're trying to understand what it is that you've done that has caused the change,

Re: [gmx-users] box size changed

Nancy, My guess is that you have pressure coupling on. Now, what is the characteristic of vacuum? What will happen if you have a balloon filled with vacuum (and one small red car of almost negligible size) and you couple it to a reference pressure (keep it out in the air)? In the other

Re: [gmx-users] box size changed

in the log file as the box size exploding. Very grateful for your advice and help!!! Nancy - Original Message - From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 28, 2007 5:15 PM Subject: Re: [gmx-users] box

Re: [gmx-users] box size changed

5:15 PM Subject: Re: [gmx-users] box size changed Nancy Deng wrote: Hi Mark, Thanks for the quick response and the funny story :) I indeed want to collect the possible comformation of a certain small molecule (a little car made of 35 atoms around 15 A in length) by MD. Since obvious to my

[gmx-users] box size changed

Dear All, I am a very beginner of Gromacs and currently trying to run two small molecule (35 atoms) MD studies, one with water and the other without water (skip the genbox step). Surprisingly, the box size of the system containing only small molecule (without water) kept shrink till the

Re: [gmx-users] box size changed

Nancy Deng wrote: Dear All, I am a very beginner of Gromacs and currently trying to run two small molecule (35 atoms) MD studies, one with water and the other without water (skip the genbox step). Surprisingly, the box size of the system containing only small molecule (without water) kept

Re: [gmx-users] box size changed

PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 28, 2007 3:42 PM Subject: Re: [gmx-users] box size changed Nancy Deng wrote: Dear All, I am a very beginner of Gromacs and currently trying to run two small molecule (35 atoms) MD studies, one

Re: [gmx-users] box size changed

Nancy Deng wrote: Hi Mark, Thanks for the quick response and the funny story :) I indeed want to collect the possible comformation of a certain small molecule (a little car made of 35 atoms around 15 A in length) by MD. Since obvious to my understanding that in vacume or in water

Re: [gmx-users] box size for simulation of membrane protein

Original Message From: Mohamed Osman [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Thursday, January 11, 2007 10:49:29 PM Subject: [gmx-users] box size for simulation of membrane protein My questions: 1. Protein is closer to one edge than the other. Does this make any difference

[gmx-users] box size for simulation of membrane protein

I am going to start by quoting: Chapter 3 of the Gromacs manual (page 14) length of each box vector must exceed the length of the macromolecule in the direction of that edge plus two times the cutoff radius RcThen it states: It is common to compormize in this respect and make the solvant