[gmx-users] RE : double sids error ? what ?!

D] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. double sids error ? what ?! (BON Michael) 2. Re: Angle definition in g_hbond ... (Mark Abraham) 3. Re: Angle definition in g_hbond ... (Dav

[gmx-users] double sids error ? what ?!

Hi all, I got a "double sids error" when using grompp. What does it mean in the first place ? Apparently, it has to do with Lincs making shake-blocks when using constraint = all-bonds. I am simulating two strands of RNA, defined in the same .top file as I want to add some distance restraint

[gmx-users] RE : FEP : separating components of dgdl

Thanks Berk, everything is fine at last. I guess this is my last question : if for example I change three bond lengths from b0A=0.1 to b0B=0.15, when I use gmxcheck with -ab, it prints only one difference between state A and B, instead of 3. Is this ok ? Maik, what is the power you are using

[gmx-users] FEP : separating components of dgdl

Thanks Maik for your parameters for amber99 soft core ! Berk, you were right. The missing term is indeed the one associated to the use of constraints=all-bonds. And yes, there was a mistake in my .top file... May I ask an other question ? I still have a warning message with grompp : "WARNING

[gmx-users] RE : FEP : separating components of dgdl

Hi, You were right for the bonds, I forgot that I was using constraints = all-bonds. Could the missing term be the soft core then ? Or is it included in VdW ? Anyway, I noticed that this problem of hidden extra term happens when I modify something else than a hydrogen. Does it make sense ? For

[gmx-users] RE: RE : FEP : separating components of dgdl (Berk Hess)

jet : gmx-users Digest, Vol 45, Issue 116 > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with

[gmx-users] RE : FEP : separating components of dgdl

ing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. Re: dihedral restraints wiki section (Behnoush Zare) 2. RE : FEP : separating components of dgdl (BON Michael)

[gmx-users] RE : FEP : separating components of dgdl

Thanks for the quick reply. I have an other question : I ran a quick simulation on a single node using mdrun -sepdvdl and the components are written in the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum of the components above. Example for some step: VdW and Coulom

[gmx-users] FEP : separating components of dgdl

Hi, I would like to know if there is a way to see the values of each components (angles, dihedrals, Coulomb...) of dgdl when performing FEP, to check whether I correctly defined the topology of state B. Many thanks, Michael Bon <>___ gmx-users maili

[gmx-users] RE : Serious mistake in the manual !

Had this mistake been done in the code too ? No, the code is correct. Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -----

[gmx-users] Serious mistake in the manual ! In the code too ?!

Hi all, In the manual 3.3, given the formula (4.99), the formula (4.100) is wrong. There is the same mistake for formula (4.102). V has the form f * g² , so V' should be f'g² + 2fgg', whereas I read f'(g²+g'g). (Well, not exactly, there is also a parsing and a sign error). Had this mistake b

[gmx-users] Drift and crash

Hi, I have been struggling for more than one month with a permanent problem in my simulations. I asked about it in previous mails in this mailing-list. Briefly, the problem is that my simulations crash at some point, and there is nothing explaining it. Nothing but a strange behaviour spotted in

[gmx-users] RE : long-term drift and crash

hael Bon Message: 2 Date: Sat, 18 Aug 2007 12:34:02 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re : long-term drift and crash To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed BON

[gmx-users] Re : long-term drift and crash

g-term drift and crash To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed BON Michael wrote: > Hi and thanks, > > The pressure is stable, the mean value is -280 bar, which sounds normal, and > it is isot

[gmx-users] RE : long-term drift and crash

ROTECTED]> Subject: Re: [gmx-users] Long-term drift, crash To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed BON Michael wrote: > Hi, > > I have been struggling for some time with a nasty problem wit

[gmx-users] Long-term drift, crash

Hi, I have been struggling for some time with a nasty problem with my simulations of RNA in water using Gromacs 3.3.1 and the AMBER ports. Nobody ever reported it so I am afraid I did some obvious mistake that I just cannot see. After some steps (between 5 and 15), my simulations crash,

[gmx-users] pb with temperature in bd (2)

I just wanted to add one thing to my previous mail, that may give some insight to a skilled Gromacs user : when I replace bd with md or sd in the .mdp, the system is correctly equilibrated with the required temperature. This problem of doubling temperature (ie 620 instead of 310) occurs only w

[gmx-users] pb with temperature in brownian dynamics

Hello everybody, I have been starting using Gromacs (3.3.1) recently and I am facing some problems. I am trying to simulate RNA with ffAMBER99, and I decided that a bd simulation would be the most efficient. My problem is maybe a known/stupid one : the temperature used during the simulation is